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seqan / seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
https://www.seqan.de
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[CRON] API-Stability #2746

Open eseiler opened 3 years ago

github-actions[bot] commented 2 years ago

Failure on gcc9

See https://github.com/seqan/seqan3/actions/runs/1299516253 for more information.

github-actions[bot] commented 2 years ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/1299516253 for more information.

github-actions[bot] commented 2 years ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/1299516253 for more information.

github-actions[bot] commented 2 years ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/1324804577 for more information.

github-actions[bot] commented 2 years ago

Failure on gcc9

See https://github.com/seqan/seqan3/actions/runs/1324804577 for more information.

github-actions[bot] commented 2 years ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/1324804577 for more information.

github-actions[bot] commented 2 years ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/1448680024 for more information.

github-actions[bot] commented 2 years ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/1448680024 for more information.

github-actions[bot] commented 2 years ago

Failure on gcc9

See https://github.com/seqan/seqan3/actions/runs/1448680024 for more information.

github-actions[bot] commented 2 years ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/1449037664 for more information.

Error 1: error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such fil ```text [ 16%] Performing patch step for 'api_stability_snippet' /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such file or directory make[2]: seqan3 seqan3-build [CMakeFiles/api_stability_snippet.dir/build.make:108: api_stability_snippet-prefix/src/api_stability_snippet-stamp/api_stability_snippet-patch] Error 128 ```
Error 2: error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such fil ```text [ 38%] Performing patch step for 'api_stability_unit' /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such file or directory make[2]: seqan3 seqan3-build [CMakeFiles/api_stability_unit.dir/build.make:108: api_stability_unit-prefix/src/api_stability_unit-stamp/api_stability_unit-patch] Error 128 ```
github-actions[bot] commented 2 years ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/1449037664 for more information.

Error 1: error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such fil ```text [ 16%] Performing patch step for 'api_stability_snippet' /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such file or directory make[2]: seqan3 seqan3-build [CMakeFiles/api_stability_snippet.dir/build.make:108: api_stability_snippet-prefix/src/api_stability_snippet-stamp/api_stability_snippet-patch] Error 128 ```
Error 2: error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such fil ```text [ 38%] Performing patch step for 'api_stability_unit' /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such file or directory make[2]: seqan3 seqan3-build [CMakeFiles/api_stability_unit.dir/build.make:108: api_stability_unit-prefix/src/api_stability_unit-stamp/api_stability_unit-patch] Error 128 ```
github-actions[bot] commented 2 years ago

Failure on gcc9

See https://github.com/seqan/seqan3/actions/runs/1449037664 for more information.

Error 1: error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such fil ```text [ 16%] Performing patch step for 'api_stability_snippet' /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such file or directory make[2]: seqan3 seqan3-build [CMakeFiles/api_stability_snippet.dir/build.make:108: api_stability_snippet-prefix/src/api_stability_snippet-stamp/api_stability_snippet-patch] Error 128 ```
Error 2: error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such fil ```text [ 38%] Performing patch step for 'api_stability_unit' /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit error: can't open patch '/home/runner/work/seqan3/seqan3/seqan3/test/api_stability/3.1.0/*.patch': No such file or directory make[2]: seqan3 seqan3-build [CMakeFiles/api_stability_unit.dir/build.make:108: api_stability_unit-prefix/src/api_stability_unit-stamp/api_stability_unit-patch] Error 128 ```
github-actions[bot] commented 2 years ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/2522574984 for more information.

Error 1: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 13%] Building CXX object CMakeFiles/search_with_user_callback_snippet.dir/search/search_with_user_callback.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp:22, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/search/search.hpp:19, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/search/search_with_user_callback.cpp:5: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 2: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 13%] Building CXX object CMakeFiles/search_snippet.dir/search/search.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp:22, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/search/search.hpp:19, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/search/search.cpp:5: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 3: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 17%] Building CXX object CMakeFiles/3.0.3_io-record_snippet.dir/release/3.0.3_io-record.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/stream/bgzf_istream.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/misc_input.hpp:28, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sequence_file/input.hpp:29, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/release/3.0.3_io-record.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 4: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 17%] Building CXX object CMakeFiles/3.0.2_lazy-search-result-range_snippet.dir/release/3.0.2_lazy-search-result-range.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp:22, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/search/search.hpp:19, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/release/3.0.2_lazy-search-result-range.cpp:8: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 5: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 17%] Building CXX object CMakeFiles/3.0.1_parallel-alignments_snippet.dir/release/3.0.1_parallel-alignments.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp:22, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/pairwise/align_pairwise.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/pairwise/all.hpp:268, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/release/3.0.1_parallel-alignments.cpp:4: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; ```
Error 6: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 17%] Building CXX object CMakeFiles/3.0.0_read-fasta-and-print-entities_snippet.dir/release/3.0.0_read-fasta-and-print-entities.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/stream/bgzf_istream.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/misc_input.hpp:28, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sequence_file/input.hpp:29, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/release/3.0.0_read-fasta-and-print-entities.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 7: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 17%] Building CXX object CMakeFiles/3.0.0_file-conversion_snippet.dir/release/3.0.0_file-conversion.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/stream/bgzf_istream.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/misc_input.hpp:28, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sequence_file/input.hpp:29, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/release/3.0.0_file-conversion.cpp:2: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 8: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 18%] Building CXX object CMakeFiles/read_mapper_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/read_mapper/read_mapper_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp:22, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/pairwise/align_pairwise.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/read_mapper/read_mapper_step3.cpp:9: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 9: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 19%] Building CXX object CMakeFiles/sam_file_input_front_snippet.dir/io/sam_file/sam_file_input_front.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/stream/bgzf_istream.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/misc_input.hpp:28, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_front.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 10: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 19%] Building CXX object CMakeFiles/sequence_file_input_file_view_snippet.dir/io/sequence_file/sequence_file_input_file_view.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/stream/bgzf_istream.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/misc_input.hpp:28, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sequence_file/input.hpp:29, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sequence_file/sequence_file_input_file_view.cpp:4: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 11: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 24%] Building CXX object CMakeFiles/align_pairwise_snippet.dir/alignment/pairwise/align_pairwise.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp:22, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/pairwise/align_pairwise.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/alignment/pairwise/align_pairwise.cpp:5: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 26%] Building CXX object CMakeFiles/sequence_file_file_conversion_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/sequence_file/sequence_file_file_conversion.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/stream/bgzf_istream.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/misc_input.hpp:28, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sequence_file/input.hpp:29, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sequence_file/all.hpp:31, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/sequence_file/sequence_file_file_conversion.cpp:25: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; ```
Error 13: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 26%] Building CXX object CMakeFiles/search_solution5_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/search/search_solution5.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp:22, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/pairwise/align_pairwise.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/search/search_solution5.cpp:2: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 14: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 26%] Building CXX object CMakeFiles/pairwise_alignment_first_global_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/pairwise_alignment/pairwise_alignment_first_global.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp:22, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/pairwise/align_pairwise.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/pairwise_alignment/pairwise_alignment_first_global.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 15: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 26%] Building CXX object CMakeFiles/structure_file_input_auto_temp_deduc_snippet.dir/io/structure_file/structure_file_input_auto_temp_deduc.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/stream/bgzf_istream.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/misc_input.hpp:28, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/structure_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/structure_file/structure_file_input_auto_temp_deduc.cpp:5: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:358:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 358 | alignas(std::hardware_destructive_interference_size) std::atomic push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:359:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 359 | alignas(std::hardware_destructive_interference_size) std::atomic pending_push_back_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:360:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 360 | alignas(std::hardware_destructive_interference_size) std::atomic ring_buffer_capacity{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:361:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 361 | alignas(std::hardware_destructive_interference_size) std::atomic_bool writer_waiting{false}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 16: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] ```text [ 26%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/sam_file/sam_file_writing.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/stream/bgzf_istream.hpp:27, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/misc_input.hpp:28, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/all.hpp:37, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/sam_file/sam_file_writing.cpp:6: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 355 | alignas(std::hardware_destructive_interference_size) std::shared_mutex mutable mutex{}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: the default value for the current CPU tuning is 64 bytes /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:355:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:356:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 356 | alignas(std::hardware_destructive_interference_size) std::atomic pop_front_position{0}; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/parallel/buffer_queue.hpp:357:18: error: use of ‘std::hardware_destructive_interference_size’ [-Werror=interference-size] 357 | alignas(std::hardware_destructive_interference_size) std::atomic pending_pop_front_position{0};
eseiler commented 2 years ago

Fixed by https://github.com/seqan/seqan3/pull/3019

github-actions[bot] commented 1 year ago

Failure on gcc11%0A---%0A%0ASee https://github.com/seqan/seqan3/actions/runs/3353906707 for more information.%0A

Error 1: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/CMakeFiles/aligned_sequence_test.dir/aligned_sequence_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/rna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0A%0A
%0A
Error 2: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/CMakeFiles/aligned_sequence_test.dir/build.make:66: alignment/CMakeFiles/aligned_sequence_test.dir/aligned_sequence_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/CMakeFiles/aligned_sequence_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2318: alignment/CMakeFiles/aligned_sequence_test.dir/all] Error 2%0AScanning dependencies of target exception_test%0A%0A
%0A
Error 3: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/CMakeFiles/exception_test.dir/exception_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/exception_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/CMakeFiles/exception_test.dir/build.make:66: alignment/CMakeFiles/exception_test.dir/exception_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/CMakeFiles/exception_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2346: alignment/CMakeFiles/exception_test.dir/all] Error 2%0AScanning dependencies of target debug_stream_alignment_test%0A%0A
%0A
Error 4: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/debug_stream_alignment_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence/debug_stream_alignment_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/build.make:66: alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/debug_stream_alignment_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2374: alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/all] Error 2%0AScanning dependencies of target align_config_vectorised_test%0A%0A
%0A
Error 5: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/align_config_vectorised_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_vectorised.hpp:16,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_vectorised_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/align_config_vectorised_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2402: alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/all] Error 2%0AScanning dependencies of target align_config_scoring_scheme_test%0A%0A
%0A
Error 6: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/align_config_scoring_scheme_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_scoring_scheme.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_scoring_scheme_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/align_config_scoring_scheme_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2430: alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/all] Error 2%0AScanning dependencies of target align_config_method_test%0A%0A
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Error 7: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_method_test.dir/align_config_method_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_method.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_method_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_method_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_method_test.dir/align_config_method_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_method_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2458: alignment/configuration/CMakeFiles/align_config_method_test.dir/all] Error 2%0AScanning dependencies of target align_config_common_test%0A%0A
%0A
Error 8: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_common_test.dir/align_config_common_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_common_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/read_mapper_indexer_step3_snippet.dir/build.make:66: CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/read_mapper_indexer_step3_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1235: CMakeFiles/read_mapper_indexer_step3_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_solution3_snippet%0A%0A
%0A
Error 9: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution3.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution3.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_solution3_snippet.dir/build.make:66: CMakeFiles/sam_file_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution3.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_solution3_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1263: CMakeFiles/sam_file_solution3_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_sam_record_snippet%0A%0A
%0A
Error 10: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_sam_record_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_sam_record.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_sam_record.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_common_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_common_test.dir/align_config_common_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_common_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2486: alignment/configuration/CMakeFiles/align_config_common_test.dir/all] Error 2%0AScanning dependencies of target align_config_on_result_test%0A%0A
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Error 11: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_on_result.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_on_result_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_on_result_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_on_result_test.dir/align_config_on_result_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_on_result_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2514: alignment/configuration/CMakeFiles/align_config_on_result_test.dir/all] Error 2%0AScanning dependencies of target align_config_gap_cost_affine_test%0A%0A
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Error 12: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/align_config_gap_cost_affine_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_gap_cost_affine.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_gap_cost_affine_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/align_config_gap_cost_affine_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2542: alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/all] Error 2%0AScanning dependencies of target align_config_min_score_test%0A%0A
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Error 13: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_min_score_test.dir/align_config_min_score_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_min_score.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_min_score_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_min_score_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_min_score_test.dir/align_config_min_score_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_min_score_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2570: alignment/configuration/CMakeFiles/align_config_min_score_test.dir/all] Error 2%0AScanning dependencies of target align_config_edit_test%0A%0A
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Error 14: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_edit_test.dir/align_config_edit_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_gap_cost_affine.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_edit.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_edit_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_edit_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_edit_test.dir/align_config_edit_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_edit_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2598: alignment/configuration/CMakeFiles/align_config_edit_test.dir/all] Error 2%0AScanning dependencies of target align_config_score_type_test%0A%0A
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Error 15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_score_type_test.dir/align_config_score_type_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_score_type.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_score_type_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_score_type_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_score_type_test.dir/align_config_score_type_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_score_type_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2626: alignment/configuration/CMakeFiles/align_config_score_type_test.dir/all] Error 2%0AScanning dependencies of target align_config_band_test%0A%0A
%0A
Error 16: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_band_test.dir/align_config_band_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_band_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_band_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_band_test.dir/align_config_band_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_band_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2654: alignment/configuration/CMakeFiles/align_config_band_test.dir/all] Error 2%0AScanning dependencies of target align_config_output_test%0A%0A
%0A
Error 17: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_output_test.dir/align_config_output_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_output.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_output_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_output_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_output_test.dir/align_config_output_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_output_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2682: alignment/configuration/CMakeFiles/align_config_output_test.dir/all] Error 2%0AScanning dependencies of target align_config_parallel_test%0A%0A
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Error 18: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_parallel_test.dir/align_config_parallel_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_parallel.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_parallel_test.cpp:14:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_parallel_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_parallel_test.dir/align_config_parallel_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_parallel_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2710: alignment/configuration/CMakeFiles/align_config_parallel_test.dir/all] Error 2%0AScanning dependencies of target gap_decorator_test%0A%0A
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Error 19: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_read_cigar_snippet.dir/build.make:66: CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_read_cigar_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1319: CMakeFiles/sam_file_read_cigar_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_filename_construction_snippet%0A%0A
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Error 20: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna16sam.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/format_bam.hpp:21,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/all.hpp:34,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_filename_construction_snippet.dir/build.make:66: CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_filename_construction_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1347: CMakeFiles/sam_file_filename_construction_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_file_extensions_snippet%0A%0A
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Error 21: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_file_extensions_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_file_extensions.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_file_extensions.cpp:2:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_file_extensions_snippet.dir/build.make:66: CMakeFiles/sam_file_file_extensions_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_file_extensions.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_file_extensions_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1375: CMakeFiles/sam_file_file_extensions_snippet.dir/all] Error 2%0AScanning dependencies of target search_solution5_snippet%0A%0A
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Error 22: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/search_solution5_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution5.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/all.hpp:31,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution5.cpp:3:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/decorator/CMakeFiles/gap_decorator_test.dir/build.make:66: alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/decorator/CMakeFiles/gap_decorator_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2738: alignment/decorator/CMakeFiles/gap_decorator_test.dir/all] Error 2%0AScanning dependencies of target pairwise_alignment_concept_test%0A%0A
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Error 23: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/pairwise_alignment_concept_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/detail/pairwise_alignment_concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/detail/pairwise_alignment_concept_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/build.make:66: alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/pairwise_alignment_concept_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2766: alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/all] Error 2%0AScanning dependencies of target alignment_trace_matrix_full_banded_test%0A%0A
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Error 24: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/alignment_trace_matrix_full_banded_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_trace_matrix_full_banded.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_trace_matrix_full_banded_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/alignment_trace_matrix_full_banded_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2794: alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/all] Error 2%0AScanning dependencies of target score_matrix_single_column_simd_test%0A%0A
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Error 25: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/score_matrix_single_column_simd_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/trace_directions.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/score_matrix_single_column_simd_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/search_solution5_snippet.dir/build.make:66: CMakeFiles/search_solution5_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution5.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/search_solution5_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1403: CMakeFiles/search_solution5_snippet.dir/all] Error 2%0AScanning dependencies of target search_solution4_snippet%0A%0A
%0A
Error 26: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/search_solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution4.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution4.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/score_matrix_single_column_simd_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2822: alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/all] Error 2%0AScanning dependencies of target alignment_score_matrix_one_column_banded_test%0A%0A
%0A
Error 27: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/alignment_score_matrix_one_column_banded_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_banded.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_score_matrix_one_column_banded_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/alignment_score_matrix_one_column_banded_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2850: alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/all] Error 2%0AScanning dependencies of target trace_iterator_test%0A%0A
%0A
Error 28: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/trace_iterator_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/trace_directions.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/trace_iterator_test.cpp:14:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/trace_iterator_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2878: alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/all] Error 2%0AScanning dependencies of target alignment_optimum_test%0A%0A
%0A
Error 29: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/alignment_optimum_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/strong_type.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_optimum.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_optimum_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/alignment_optimum_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2906: alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/all] Error 2%0AScanning dependencies of target alignment_matrix_column_major_range_base_test%0A%0A
%0A
Error 30: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/alignment_matrix_column_major_range_base_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/iterator_traits.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/range/type_traits.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_matrix_column_major_range_base_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/search_solution4_snippet.dir/build.make:66: CMakeFiles/search_solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution4.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/search_solution4_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1431: CMakeFiles/search_solution4_snippet.dir/all] Error 2%0AScanning dependencies of target search_solution3_snippet%0A%0A
%0A
Error 31: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/search_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution3.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution3.cpp:3:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/alignment_matrix_column_major_range_base_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2934: alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/all] Error 2%0AScanning dependencies of target advanceable_alignment_coordinate_test%0A%0A
%0A
Error 32: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/advanceable_alignment_coordinate_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/strong_type.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/advanceable_alignment_coordinate_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/advanceable_alignment_coordinate_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2962: alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/all] Error 2%0AScanning dependencies of target debug_stream_debug_matrix_test%0A%0A
%0A
Error 33: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 4%25] Building CXX object alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/debug_stream_debug_matrix_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/strong_type.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/matrix_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/debug_matrix.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/debug_stream_debug_matrix_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/debug_stream_debug_matrix_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2990: alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/all] Error 2%0AScanning dependencies of target combined_score_and_trace_matrix_test%0A%0A
%0A
Error 34: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 4%25] Building CXX object alignment/matrix/detail/CMakeFiles/combined_score_and_trace_matrix_test.dir/combined_score_and_trace_matrix_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/trace_directions.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/combined_score_and_trace_matrix_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/search_solution3_snippet.dir/build.make:66: CMakeFiles/search_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution3.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/search_solution3_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1459: CMakeFiles/search_solution3_snippet.dir/all] Error 2%0AScanning dependencies of target search_solution2_snippet%0A%0A
%0A
Error 35: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0A```text%0A[ 2%25] Building CXX object CMakeFiles/search_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution2.cpp.o%0Acc1plus: all warnings being treated as errors%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution2.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:1

github-actions[bot] commented 1 year ago

Failure on gcc12%0A---%0A%0ASee https://github.com/seqan/seqan3/actions/runs/3353906707 for more information.%0A

Error 1: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Built target gtest_main%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/rna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0AScanning dependencies of target read_mapper_indexer_step3_snippet%0A%0A
%0A
Error 2: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/CMakeFiles/aligned_sequence_test.dir/build.make:66: alignment/CMakeFiles/aligned_sequence_test.dir/aligned_sequence_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/CMakeFiles/aligned_sequence_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2318: alignment/CMakeFiles/aligned_sequence_test.dir/all] Error 2%0AScanning dependencies of target exception_test%0A%0A
%0A
Error 3: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 0%25] Building CXX object alignment/CMakeFiles/exception_test.dir/exception_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/exception_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/CMakeFiles/exception_test.dir/build.make:66: alignment/CMakeFiles/exception_test.dir/exception_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/CMakeFiles/exception_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2346: alignment/CMakeFiles/exception_test.dir/all] Error 2%0AScanning dependencies of target debug_stream_alignment_test%0A%0A
%0A
Error 4: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 0%25] Building CXX object alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/debug_stream_alignment_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence/debug_stream_alignment_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/build.make:66: alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/debug_stream_alignment_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2374: alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/all] Error 2%0AScanning dependencies of target align_config_vectorised_test%0A%0A
%0A
Error 5: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/align_config_vectorised_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_vectorised.hpp:16,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_vectorised_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/align_config_vectorised_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2402: alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/all] Error 2%0AScanning dependencies of target align_config_scoring_scheme_test%0A%0A
%0A
Error 6: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/align_config_scoring_scheme_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_scoring_scheme.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_scoring_scheme_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/align_config_scoring_scheme_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2430: alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/all] Error 2%0AScanning dependencies of target align_config_method_test%0A%0A
%0A
Error 7: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_method_test.dir/align_config_method_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_method.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_method_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_method_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_method_test.dir/align_config_method_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_method_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2458: alignment/configuration/CMakeFiles/align_config_method_test.dir/all] Error 2%0AScanning dependencies of target align_config_common_test%0A%0A
%0A
Error 8: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_common_test.dir/align_config_common_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_common_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/read_mapper_indexer_step3_snippet.dir/build.make:66: CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/read_mapper_indexer_step3_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1235: CMakeFiles/read_mapper_indexer_step3_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_solution3_snippet%0A%0A
%0A
Error 9: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution3.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution3.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_solution3_snippet.dir/build.make:66: CMakeFiles/sam_file_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution3.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_solution3_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1263: CMakeFiles/sam_file_solution3_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_sam_record_snippet%0A%0A
%0A
Error 10: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_sam_record_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_sam_record.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_sam_record.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_sam_record_snippet.dir/build.make:66: CMakeFiles/sam_file_sam_record_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_sam_record.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_sam_record_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1291: CMakeFiles/sam_file_sam_record_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_read_cigar_snippet%0A%0A
%0A
Error 11: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_common_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_common_test.dir/align_config_common_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_common_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2486: alignment/configuration/CMakeFiles/align_config_common_test.dir/all] Error 2%0AScanning dependencies of target align_config_on_result_test%0A%0A
%0A
Error 12: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_on_result_test.dir/align_config_on_result_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_on_result.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_on_result_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_on_result_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_on_result_test.dir/align_config_on_result_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_on_result_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2514: alignment/configuration/CMakeFiles/align_config_on_result_test.dir/all] Error 2%0AScanning dependencies of target align_config_gap_cost_affine_test%0A%0A
%0A
Error 13: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/align_config_gap_cost_affine_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_gap_cost_affine.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_gap_cost_affine_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/align_config_gap_cost_affine_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2542: alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/all] Error 2%0AScanning dependencies of target align_config_min_score_test%0A%0A
%0A
Error 14: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_min_score_test.dir/align_config_min_score_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_min_score.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_min_score_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_min_score_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_min_score_test.dir/align_config_min_score_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_min_score_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2570: alignment/configuration/CMakeFiles/align_config_min_score_test.dir/all] Error 2%0AScanning dependencies of target align_config_edit_test%0A%0A
%0A
Error 15: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_edit_test.dir/align_config_edit_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_gap_cost_affine.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_edit.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_edit_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_edit_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_edit_test.dir/align_config_edit_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_edit_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2598: alignment/configuration/CMakeFiles/align_config_edit_test.dir/all] Error 2%0AScanning dependencies of target align_config_score_type_test%0A%0A
%0A
Error 16: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_score_type_test.dir/align_config_score_type_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_score_type.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_score_type_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_score_type_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_score_type_test.dir/align_config_score_type_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_score_type_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2626: alignment/configuration/CMakeFiles/align_config_score_type_test.dir/all] Error 2%0AScanning dependencies of target align_config_band_test%0A%0A
%0A
Error 17: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_band_test.dir/align_config_band_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_band_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_band_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_band_test.dir/align_config_band_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_band_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2654: alignment/configuration/CMakeFiles/align_config_band_test.dir/all] Error 2%0AScanning dependencies of target align_config_output_test%0A%0A
%0A
Error 18: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_output_test.dir/align_config_output_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_output.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_output_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_output_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_output_test.dir/align_config_output_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_output_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2682: alignment/configuration/CMakeFiles/align_config_output_test.dir/all] Error 2%0AScanning dependencies of target align_config_parallel_test%0A%0A
%0A
Error 19: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_parallel_test.dir/align_config_parallel_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_parallel.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_parallel_test.cpp:14:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_parallel_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_parallel_test.dir/align_config_parallel_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_parallel_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2710: alignment/configuration/CMakeFiles/align_config_parallel_test.dir/all] Error 2%0AScanning dependencies of target gap_decorator_test%0A%0A
%0A
Error 20: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna16sam.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/format_bam.hpp:21,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/all.hpp:34,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_filename_construction_snippet.dir/build.make:66: CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_filename_construction_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1347: CMakeFiles/sam_file_filename_construction_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_file_extensions_snippet%0A%0A
%0A
Error 21: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_file_extensions_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_file_extensions.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_file_extensions.cpp:2:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_file_extensions_snippet.dir/build.make:66: CMakeFiles/sam_file_file_extensions_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_file_extensions.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_file_extensions_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1375: CMakeFiles/sam_file_file_extensions_snippet.dir/all] Error 2%0AScanning dependencies of target search_solution5_snippet%0A%0A
%0A
Error 22: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/search_solution5_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution5.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/all.hpp:31,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution5.cpp:3:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/decorator/CMakeFiles/gap_decorator_test.dir/build.make:66: alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/decorator/CMakeFiles/gap_decorator_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2738: alignment/decorator/CMakeFiles/gap_decorator_test.dir/all] Error 2%0AScanning dependencies of target pairwise_alignment_concept_test%0A%0A
%0A
Error 23: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 1%25] Building CXX object alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/pairwise_alignment_concept_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/detail/pairwise_alignment_concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/detail/pairwise_alignment_concept_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/build.make:66: alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/pairwise_alignment_concept_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2766: alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/all] Error 2%0AScanning dependencies of target alignment_trace_matrix_full_banded_test%0A%0A
%0A
Error 24: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/alignment_trace_matrix_full_banded_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_trace_matrix_full_banded.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_trace_matrix_full_banded_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/alignment_trace_matrix_full_banded_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2794: alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/all] Error 2%0AScanning dependencies of target score_matrix_single_column_simd_test%0A%0A
%0A
Error 25: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/score_matrix_single_column_simd_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/trace_directions.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/score_matrix_single_column_simd_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/search_solution5_snippet.dir/build.make:66: CMakeFiles/search_solution5_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution5.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/search_solution5_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1403: CMakeFiles/search_solution5_snippet.dir/all] Error 2%0AScanning dependencies of target search_solution4_snippet%0A%0A
%0A
Error 26: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/search_solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution4.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution4.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/score_matrix_single_column_simd_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2822: alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/all] Error 2%0AScanning dependencies of target alignment_score_matrix_one_column_banded_test%0A%0A
%0A
Error 27: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/alignment_score_matrix_one_column_banded_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_banded.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_score_matrix_one_column_banded_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/alignment_score_matrix_one_column_banded_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2850: alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/all] Error 2%0AScanning dependencies of target trace_iterator_test%0A%0A
%0A
Error 28: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A%0A```text%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/trace_iterator_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/trace_directions.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/trace_iterator_test.cpp:14:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:78:29: error: Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile. [-Werror]%0A 78 | # pragma GCC warning "Be aware that GCC < 12.2 might have bugs that cause SeqAn3 fail to compile."%0A | ^~~~~~~~~~~~~~~~~%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(GNUC > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/trace_iteratortest.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/trace

github-actions[bot] commented 1 year ago

Failure on gcc10%0A---%0A%0ASee https://github.com/seqan/seqan3/actions/runs/3353906707 for more information.%0A

Error 1: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/rna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/CMakeFiles/aligned_sequence_test.dir/build.make:66: alignment/CMakeFiles/aligned_sequence_test.dir/aligned_sequence_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/CMakeFiles/aligned_sequence_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2318: alignment/CMakeFiles/aligned_sequence_test.dir/all] Error 2%0AScanning dependencies of target exception_test%0A%0A
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Error 2: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/CMakeFiles/exception_test.dir/exception_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/exception_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/CMakeFiles/exception_test.dir/build.make:66: alignment/CMakeFiles/exception_test.dir/exception_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/CMakeFiles/exception_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2346: alignment/CMakeFiles/exception_test.dir/all] Error 2%0AScanning dependencies of target debug_stream_alignment_test%0A%0A
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Error 3: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/debug_stream_alignment_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence/debug_stream_alignment_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/build.make:66: alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/debug_stream_alignment_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2374: alignment/aligned_sequence/CMakeFiles/debug_stream_alignment_test.dir/all] Error 2%0AScanning dependencies of target align_config_vectorised_test%0A%0A
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Error 4: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/align_config_vectorised_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_vectorised.hpp:16,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_vectorised_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/align_config_vectorised_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2402: alignment/configuration/CMakeFiles/align_config_vectorised_test.dir/all] Error 2%0AScanning dependencies of target align_config_scoring_scheme_test%0A%0A
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Error 5: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/align_config_scoring_scheme_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_scoring_scheme.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_scoring_scheme_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/align_config_scoring_scheme_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2430: alignment/configuration/CMakeFiles/align_config_scoring_scheme_test.dir/all] Error 2%0AScanning dependencies of target align_config_method_test%0A%0A
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Error 6: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_method_test.dir/align_config_method_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_method.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_method_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_method_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_method_test.dir/align_config_method_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_method_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2458: alignment/configuration/CMakeFiles/align_config_method_test.dir/all] Error 2%0AScanning dependencies of target align_config_common_test%0A%0A
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Error 7: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_common_test.dir/align_config_common_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_common_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/read_mapper_indexer_step3_snippet.dir/build.make:66: CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/read_mapper_indexer_step3_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1235: CMakeFiles/read_mapper_indexer_step3_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_solution3_snippet%0A%0A
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Error 8: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution3.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution3.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_solution3_snippet.dir/build.make:66: CMakeFiles/sam_file_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution3.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_solution3_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1263: CMakeFiles/sam_file_solution3_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_sam_record_snippet%0A%0A
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Error 9: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_sam_record_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_sam_record.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_sam_record.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_common_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_common_test.dir/align_config_common_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_common_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2486: alignment/configuration/CMakeFiles/align_config_common_test.dir/all] Error 2%0AScanning dependencies of target align_config_on_result_test%0A%0A
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Error 10: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_on_result_test.dir/align_config_on_result_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_on_result.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_on_result_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_on_result_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_on_result_test.dir/align_config_on_result_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_on_result_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2514: alignment/configuration/CMakeFiles/align_config_on_result_test.dir/all] Error 2%0AScanning dependencies of target align_config_gap_cost_affine_test%0A%0A
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Error 11: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/align_config_gap_cost_affine_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_gap_cost_affine.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_gap_cost_affine_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/align_config_gap_cost_affine_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2542: alignment/configuration/CMakeFiles/align_config_gap_cost_affine_test.dir/all] Error 2%0AScanning dependencies of target align_config_min_score_test%0A%0A
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Error 12: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 0%25] Building CXX object alignment/configuration/CMakeFiles/align_config_min_score_test.dir/align_config_min_score_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_min_score.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_min_score_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_min_score_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_min_score_test.dir/align_config_min_score_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_min_score_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2570: alignment/configuration/CMakeFiles/align_config_min_score_test.dir/all] Error 2%0AScanning dependencies of target align_config_edit_test%0A%0A
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Error 13: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_edit_test.dir/align_config_edit_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_gap_cost_affine.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_edit.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_edit_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_edit_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_edit_test.dir/align_config_edit_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_edit_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2598: alignment/configuration/CMakeFiles/align_config_edit_test.dir/all] Error 2%0AScanning dependencies of target align_config_score_type_test%0A%0A
%0A
Error 14: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_score_type_test.dir/align_config_score_type_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_score_type.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_score_type_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_score_type_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_score_type_test.dir/align_config_score_type_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_score_type_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2626: alignment/configuration/CMakeFiles/align_config_score_type_test.dir/all] Error 2%0AScanning dependencies of target align_config_band_test%0A%0A
%0A
Error 15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_band_test.dir/align_config_band_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_band_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_band_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_band_test.dir/align_config_band_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_band_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2654: alignment/configuration/CMakeFiles/align_config_band_test.dir/all] Error 2%0AScanning dependencies of target align_config_output_test%0A%0A
%0A
Error 16: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_output_test.dir/align_config_output_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_output.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_output_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_output_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_output_test.dir/align_config_output_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_output_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2682: alignment/configuration/CMakeFiles/align_config_output_test.dir/all] Error 2%0AScanning dependencies of target align_config_parallel_test%0A%0A
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Error 17: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/configuration/CMakeFiles/align_config_parallel_test.dir/align_config_parallel_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_parallel.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/configuration/align_config_parallel_test.cpp:14:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_sam_record_snippet.dir/build.make:66: CMakeFiles/sam_file_sam_record_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_sam_record.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_sam_record_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1291: CMakeFiles/sam_file_sam_record_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_read_cigar_snippet%0A%0A
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Error 18: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/configuration/CMakeFiles/align_config_parallel_test.dir/build.make:66: alignment/configuration/CMakeFiles/align_config_parallel_test.dir/align_config_parallel_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/configuration/CMakeFiles/align_config_parallel_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2710: alignment/configuration/CMakeFiles/align_config_parallel_test.dir/all] Error 2%0AScanning dependencies of target gap_decorator_test%0A%0A
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Error 19: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/decorator/CMakeFiles/gap_decorator_test.dir/build.make:66: alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/decorator/CMakeFiles/gap_decorator_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2738: alignment/decorator/CMakeFiles/gap_decorator_test.dir/all] Error 2%0AScanning dependencies of target pairwise_alignment_concept_test%0A%0A
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Error 20: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 1%25] Building CXX object alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/pairwise_alignment_concept_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/detail/pairwise_alignment_concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/detail/pairwise_alignment_concept_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/build.make:66: alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/pairwise_alignment_concept_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2766: alignment/detail/CMakeFiles/pairwise_alignment_concept_test.dir/all] Error 2%0AScanning dependencies of target alignment_trace_matrix_full_banded_test%0A%0A
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Error 21: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/alignment_trace_matrix_full_banded_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_trace_matrix_full_banded.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_trace_matrix_full_banded_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_read_cigar_snippet.dir/build.make:66: CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_read_cigar_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1319: CMakeFiles/sam_file_read_cigar_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_filename_construction_snippet%0A%0A
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Error 22: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna16sam.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/format_bam.hpp:21,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/all.hpp:34,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/alignment_trace_matrix_full_banded_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2794: alignment/matrix/detail/CMakeFiles/alignment_trace_matrix_full_banded_test.dir/all] Error 2%0AScanning dependencies of target score_matrix_single_column_simd_test%0A%0A
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Error 23: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/score_matrix_single_column_simd_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/trace_directions.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/score_matrix_single_column_simd_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_filename_construction_snippet.dir/build.make:66: CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_filename_construction_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1347: CMakeFiles/sam_file_filename_construction_snippet.dir/all] Error 2%0AScanning dependencies of target sam_file_file_extensions_snippet%0A%0A
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Error 24: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/sam_file_file_extensions_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_file_extensions.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_file_extensions.cpp:2:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/score_matrix_single_column_simd_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2822: alignment/matrix/detail/CMakeFiles/score_matrix_single_column_simd_test.dir/all] Error 2%0AScanning dependencies of target alignment_score_matrix_one_column_banded_test%0A%0A
%0A
Error 25: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/alignment_score_matrix_one_column_banded_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_banded.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_score_matrix_one_column_banded_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/sam_file_file_extensions_snippet.dir/build.make:66: CMakeFiles/sam_file_file_extensions_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_file_extensions.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/sam_file_file_extensions_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1375: CMakeFiles/sam_file_file_extensions_snippet.dir/all] Error 2%0AScanning dependencies of target search_solution5_snippet%0A%0A
%0A
Error 26: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/search_solution5_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution5.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/template_inspection.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/configuration/detail/concept.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/detail.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/align_config_band.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/configuration/all.hpp:31,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution5.cpp:3:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/alignment_score_matrix_one_column_banded_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2850: alignment/matrix/detail/CMakeFiles/alignment_score_matrix_one_column_banded_test.dir/all] Error 2%0AScanning dependencies of target trace_iterator_test%0A%0A
%0A
Error 27: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/trace_iterator_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/trace_directions.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/trace_iterator_test.cpp:14:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/trace_iterator_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2878: alignment/matrix/detail/CMakeFiles/trace_iterator_test.dir/all] Error 2%0AScanning dependencies of target alignment_optimum_test%0A%0A
%0A
Error 28: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/alignment_optimum_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/strong_type.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_optimum.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_optimum_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/alignment_optimum_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2906: alignment/matrix/detail/CMakeFiles/alignment_optimum_test.dir/all] Error 2%0AScanning dependencies of target alignment_matrix_column_major_range_base_test%0A%0A
%0A
Error 29: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/alignment_matrix_column_major_range_base_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/iterator_traits.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/range/type_traits.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp:20,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/alignment_matrix_column_major_range_base_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/alignment_matrix_column_major_range_base_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2934: alignment/matrix/detail/CMakeFiles/alignment_matrix_column_major_range_base_test.dir/all] Error 2%0AScanning dependencies of target advanceable_alignment_coordinate_test%0A%0A
%0A
Error 30: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 3%25] Building CXX object alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/advanceable_alignment_coordinate_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/strong_type.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/advanceable_alignment_coordinate_test.cpp:12:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/advanceable_alignment_coordinate_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2962: alignment/matrix/detail/CMakeFiles/advanceable_alignment_coordinate_test.dir/all] Error 2%0AScanning dependencies of target debug_stream_debug_matrix_test%0A%0A
%0A
Error 31: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 4%25] Building CXX object alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/debug_stream_debug_matrix_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/detail/strong_type.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp:18,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/matrix_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/debug_matrix.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/debug_stream_debug_matrix_test.cpp:10:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/debug_stream_debug_matrix_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:2990: alignment/matrix/detail/CMakeFiles/debug_stream_debug_matrix_test.dir/all] Error 2%0AScanning dependencies of target combined_score_and_trace_matrix_test%0A%0A
%0A
Error 32: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 4%25] Building CXX object alignment/matrix/detail/CMakeFiles/combined_score_and_trace_matrix_test.dir/combined_score_and_trace_matrix_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/add_enum_bitwise_operators.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/trace_directions.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/matrix/detail/combined_score_and_trace_matrix_test.cpp:13:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/search_solution5_snippet.dir/build.make:66: CMakeFiles/search_solution5_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution5.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/search_solution5_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1403: CMakeFiles/search_solution5_snippet.dir/all] Error 2%0AScanning dependencies of target search_solution4_snippet%0A%0A
%0A
Error 33: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/search_solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution4.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution4.cpp:1:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [CMakeFiles/search_solution4_snippet.dir/build.make:66: CMakeFiles/search_solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution4.cpp.o] Error 1%0Agmake[5]: Target 'CMakeFiles/search_solution4_snippet.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:1431: CMakeFiles/search_solution4_snippet.dir/all] Error 2%0AScanning dependencies of target search_solution3_snippet%0A%0A
%0A
Error 34: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0Atext%0A[ 2%25] Building CXX object CMakeFiles/search_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution3.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/exception.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/concept.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/alphabet_base.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/nucleotide_base.hpp:15,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/nucleotide/dna4.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_solution3.cpp:3:%0A/home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/platform.hpp:90:15: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A 90 | # endif(__GNUC__ > 12)%0A | ^%0Acc1plus: all warnings being treated as errors%0Agmake[5]: *** [alignment/matrix/detail/CMakeFiles/combined_score_and_trace_matrix_test.dir/build.make:66: alignment/matrix/detail/CMakeFiles/combined_score_and_trace_matrix_test.dir/combined_score_and_trace_matrix_test.cpp.o] Error 1%0Agmake[5]: Target 'alignment/matrix/detail/CMakeFiles/combined_score_and_trace_matrix_test.dir/build' not remade because of errors.%0Agmake[4]: *** [CMakeFiles/Makefile2:3018: alignment/matrix/detail/CMakeFiles/combined_score_and_trace_matrix_test.dir/all] Error 2%0AScanning dependencies of target aligned_sequence_builder_test%0A%0A
%0A
Error 35: error: extra tokens at end of #endif directive [-Werror=endif-labels]%0A%0A```text%0A[ 4%25] Building CXX object alignment/matrix/detail/CMakeFiles/aligned_sequence_builder_test.dir/aligned_sequence_builder_test.cpp.o%0AIn file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/exception.hpp:17,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp:19,%0A from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/matrix/detail/aligned_sequence_builder.hpp:20,%0A

github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3402658315 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 2%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 2%] Building CXX object CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 17%] Building CXX object alignment/pairwise/CMakeFiles/alignment_result_test.dir/alignment_result_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/pairwise/alignment_result_test.cpp:22:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 22 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]: *** [alignment/pairwise/CMakeFiles/alignment_result_test.dir/build.make:66: alignment/pairwise/CMakeFiles/alignment_result_test.dir/alignment_result_test.cpp.o] Error 1 gmake[5]: Target 'alignment/pairwise/CMakeFiles/alignment_result_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:3802: alignment/pairwise/CMakeFiles/alignment_result_test.dir/all] Error 2 Scanning dependencies of target align_result_selector_test ```
Error 4: error: invalid use of void expression ```text [ 23%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5603: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 5: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the docu ```text [ 21%] Building CXX object alignment/pairwise/edit_distance/CMakeFiles/global_edit_distance_unbanded_test.dir/global_edit_distance_unbanded_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 104 | []() constexpr | ~~~~~~~~~~~~~~ 105 | { | ~ 106 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 | return false; | ~~~~~~~~~~~~~ 109 | return true; | ~~~~~~~~~~~~ 110 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5827: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 6: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please ```text [ 63%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:19: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 | return false; | ~~~~~~~~~~~~~ 380 | return true; | ~~~~~~~~~~~~ 381 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 5, std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 5; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 4, std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional >’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 4; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional}]’ ```
Error 7: error: invalid use of void expression ```text [ 69%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12266: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 8: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 72%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12518: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 9: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 53%] Building CXX object core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/algorithm_executor_blocking_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/algorithm_executor_blocking_test.cpp:15:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 15 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]: *** [core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/build.make:66: core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/algorithm_executor_blocking_test.cpp.o] Error 1 gmake[5]: Target 'core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:6938: core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/all] Error 2 Scanning dependencies of target execution_handler_sequential_test ```
Error 10: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 55%] Building CXX object core/detail/CMakeFiles/persist_view_test.dir/persist_view_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/detail/persist_view_test.cpp:15:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 15 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]: *** [core/detail/CMakeFiles/persist_view_test.dir/build.make:66: core/detail/CMakeFiles/persist_view_test.dir/persist_view_test.cpp.o] Error 1 gmake[5]: Target 'core/detail/CMakeFiles/persist_view_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7134: core/detail/CMakeFiles/persist_view_test.dir/all] Error 2 Scanning dependencies of target deferred_crtp_base_test ```
Error 11: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the docu ```text [ 73%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 104 | []() constexpr | ~~~~~~~~~~~~~~ 105 | { | ~ 106 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 | return false; | ~~~~~~~~~~~~~ 109 | return true; | ~~~~~~~~~~~~ 110 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: ```
Error 12: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please ```text [ 73%] Building CXX object CMakeFiles/sam_file_output_format_construction_snippet.dir/io/sam_file/sam_file_output_format_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:19: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 | return false; | ~~~~~~~~~~~~~ 380 | return true; | ~~~~~~~~~~~~ 381 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:386:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ ```
Error 13: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 73%] Building CXX object CMakeFiles/sam_file_output_io_pipeline_snippet.dir/io/sam_file/sam_file_output_io_pipeline.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:632:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:370:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:837:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 837 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:838:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 838 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:862:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 862 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:863:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 863 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 14: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:19: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) ```
Error 15: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the docu ```text [ 74%] Building CXX object CMakeFiles/structure_file_output_push_back_snippet.dir/io/structure_file/structure_file_output_push_back.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 104 | []() constexpr | ~~~~~~~~~~~~~~ 105 | { | ~ 106 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 | return false; | ~~~~~~~~~~~~~ 109 | return true; | ~~~~~~~~~~~~ 110 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], ```
Error 16: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:222:77: error: invalid use of void expression 222 | EXPECT_SAME_TYPE(alignment_t const &, decltype(std::as_const(r.alignment()))); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:222:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 222 | EXPECT_SAME_TYPE(alignment_t const &, decltype(std::as_const(r.alignment()))); | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:222:77: error: invalid use of void expression 222 | EXPECT_SAME_TYPE(alignment_t const &, decltype(std::as_const(r.alignment()))); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ ```
Error 17: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3402658315 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 2%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 4%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 3: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 17%] Building CXX object alignment/pairwise/CMakeFiles/alignment_result_test.dir/alignment_result_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/pairwise/alignment_result_test.cpp:22:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 22 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]: *** [alignment/pairwise/CMakeFiles/alignment_result_test.dir/build.make:66: alignment/pairwise/CMakeFiles/alignment_result_test.dir/alignment_result_test.cpp.o] Error 1 gmake[5]: Target 'alignment/pairwise/CMakeFiles/alignment_result_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:3802: alignment/pairwise/CMakeFiles/alignment_result_test.dir/all] Error 2 Scanning dependencies of target align_result_selector_test ```
Error 4: error: invalid use of void expression ```text [ 23%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5603: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 5: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the docu ```text [ 26%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 104 | []() constexpr | ~~~~~~~~~~~~~~ 105 | { | ~ 106 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 | return false; | ~~~~~~~~~~~~~ 109 | return true; | ~~~~~~~~~~~~ 110 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 6: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please ```text [ 63%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:48: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 | return false; | ~~~~~~~~~~~~~ 380 | return true; | ~~~~~~~~~~~~ 381 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 5, std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 5; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 4, std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional >’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 4; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 3, std::vector >, std::__cxx11::basic_string, std::allocator >, int>’ ```
Error 7: error: invalid use of void expression ```text [ 69%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12266: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 8: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 72%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12518: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 9: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 53%] Building CXX object core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/algorithm_executor_blocking_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/algorithm_executor_blocking_test.cpp:15:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 15 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]: *** [core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/build.make:66: core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/algorithm_executor_blocking_test.cpp.o] Error 1 gmake[5]: Target 'core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:6938: core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/all] Error 2 Scanning dependencies of target execution_handler_sequential_test ```
Error 10: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 73%] Building CXX object CMakeFiles/sam_file_input_reading_range_based_for_loop_snippet.dir/io/sam_file/sam_file_input_reading_range_based_for_loop.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/detail/persist_view_test.cpp:15:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 15 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]: *** [core/detail/CMakeFiles/persist_view_test.dir/build.make:66: core/detail/CMakeFiles/persist_view_test.dir/persist_view_test.cpp.o] Error 1 gmake[5]: Target 'core/detail/CMakeFiles/persist_view_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7134: core/detail/CMakeFiles/persist_view_test.dir/all] Error 2 Scanning dependencies of target deferred_crtp_base_test ```
Error 11: error: no match for ‘operator<<’ ```text [ 56%] Building CXX object io/CMakeFiles/record_test.dir/record_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 12: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the docu ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 104 | []() constexpr | ~~~~~~~~~~~~~~ 105 | { | ~ 106 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 | return false; | ~~~~~~~~~~~~~ 109 | return true; | ~~~~~~~~~~~~ 110 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 13: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please ```text [ 74%] Building CXX object CMakeFiles/read_mapper_step2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step2.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:48: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 | return false; | ~~~~~~~~~~~~~ 380 | return true; | ~~~~~~~~~~~~ 381 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:386:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 14: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:48: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) ```
Error 15: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:222:77: error: invalid use of void expression 222 | EXPECT_SAME_TYPE(alignment_t const &, decltype(std::as_const(r.alignment()))); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:222:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 222 | EXPECT_SAME_TYPE(alignment_t const &, decltype(std::as_const(r.alignment()))); | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:222:77: error: invalid use of void expression 222 | EXPECT_SAME_TYPE(alignment_t const &, decltype(std::as_const(r.alignment()))); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ ```
Error 16: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7890: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 17: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please ```text [ 75%] Building CXX object CMakeFiles/minimisers_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/minimisers_solution3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:48: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 | return false; | ~~~~~~~~~~~~~ 380 | return true; | ~~~~~~~~~~~~ 381 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:386:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), ```
Error 18: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 75%] Building CXX object CMakeFiles/sequence_file_input_istringstream_snippet.dir/io/sequence_file/sequence_file_input_istringstream.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sequence_file/sequence_file_integration_no_performance_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sequence_file/sequence_file_integration_test.cpp:13:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 13 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]:
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3402658315 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 2%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 2%] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 17%] Building CXX object alignment/pairwise/CMakeFiles/alignment_result_test.dir/alignment_result_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/pairwise/alignment_result_test.cpp:22:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 22 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]: *** [alignment/pairwise/CMakeFiles/alignment_result_test.dir/build.make:66: alignment/pairwise/CMakeFiles/alignment_result_test.dir/alignment_result_test.cpp.o] Error 1 gmake[5]: Target 'alignment/pairwise/CMakeFiles/alignment_result_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:3802: alignment/pairwise/CMakeFiles/alignment_result_test.dir/all] Error 2 Scanning dependencies of target align_result_selector_test ```
Error 4: error: invalid use of void expression ```text [ 23%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5603: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 5: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the docu ```text [ 26%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 104 | []() constexpr | ~~~~~~~~~~~~~~ 105 | { | ~ 106 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 | return false; | ~~~~~~~~~~~~~ 109 | return true; | ~~~~~~~~~~~~ 110 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5827: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 6: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please ```text [ 37%] Building CXX object alphabet/quality/CMakeFiles/phred94_test.dir/phred94_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:19: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 | return false; | ~~~~~~~~~~~~~ 380 | return true; | ~~~~~~~~~~~~ 381 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 5, std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 5; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 4, std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional >’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 4; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >, int, std::optional}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 3, std::vector >, std::__cxx11::basic_string, std::allocator >, int>’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] ```
Error 7: error: invalid use of void expression ```text [ 43%] Building CXX object alphabet/views/CMakeFiles/translate_join_test.dir/translate_join_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12266: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 8: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 72%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12518: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 9: error: no match for ‘operator<<’ ```text [ 45%] Building CXX object argument_parser/detail/CMakeFiles/version_check_release_test.dir/version_check_release_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 10: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 53%] Building CXX object core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/algorithm_executor_blocking_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/algorithm_executor_blocking_test.cpp:15:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 15 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]: *** [core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/build.make:66: core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/algorithm_executor_blocking_test.cpp.o] Error 1 gmake[5]: Target 'core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:6938: core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/all] Error 2 Scanning dependencies of target execution_handler_sequential_test ```
Error 11: error: seqan3/core/detail/persist_view.hpp: No such file or directory ```text [ 55%] Building CXX object core/detail/CMakeFiles/persist_view_test.dir/persist_view_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/detail/persist_view_test.cpp:15:10: fatal error: seqan3/core/detail/persist_view.hpp: No such file or directory 15 | #include | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[5]: *** [core/detail/CMakeFiles/persist_view_test.dir/build.make:66: core/detail/CMakeFiles/persist_view_test.dir/persist_view_test.cpp.o] Error 1 gmake[5]: Target 'core/detail/CMakeFiles/persist_view_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7134: core/detail/CMakeFiles/persist_view_test.dir/all] Error 2 Scanning dependencies of target deferred_crtp_base_test ```
Error 12: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the docu ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 104 | []() constexpr | ~~~~~~~~~~~~~~ 105 | { | ~ 106 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 | return false; | ~~~~~~~~~~~~~ 109 | return true; | ~~~~~~~~~~~~ 110 | }(), | ~^~ ```
Error 13: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please ```text [ 76%] Building CXX object CMakeFiles/sequence_file_output_emplace_back_snippet.dir/io/sequence_file/sequence_file_output_emplace_back.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:19: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 | return false; | ~~~~~~~~~~~~~ 380 | return true; | ~~~~~~~~~~~~ 381 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, int, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:386:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 14: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 77%] Building CXX object CMakeFiles/structure_file_input_arg_spec_snippet.dir/io/structure_file/structure_file_input_arg_spec.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:632:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:370:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:837:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 837 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:838:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 838 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:862:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 862 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:863:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 863 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 15: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 77%] Building CXX object CMakeFiles/sequence_file_output_range_interface_snippet.dir/io/sequence_file/sequence_file_output_range_interface.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 16: error: invalid use of void expression ```text [ 78%] Building CXX object CMakeFiles/sequence_file_output_record_wise_iteration_snippet.dir/io/sequence_file/sequence_file_output_record_wise_iteration.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:370:19: error: static assertion failed: The field::alignment is deprecated and only field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 370 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:381:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 375 | []() constexpr | ~~~~~~~~~~~~~~ 376 | { | ~ 377 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 17: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 78%] Building CXX object CMakeFiles/sequence_file_output_template_deduction_snippet.dir/io/sequence_file/sequence_file_output_template_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits<>; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:632:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits<>; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:572:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:837:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 837 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:838:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 838 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:862:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 862 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:863:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 863 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 18: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the docu ```text [ 78%] Building CXX object CMakeFiles/sequence_file_piping_in_out_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/07_sequence_file/sequence_file_piping_in_out.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:110:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 104 | []() constexpr | ~~~~~~~~~~~~~~ 105 | { | ~ 106 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 | return false; | ~
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3453557336 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: ```
Error 6: error: invalid use of void expression ```text [ 46%] Building CXX object argument_parser/detail/CMakeFiles/format_man_test.dir/format_man_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 75%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/read_mapper_step2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step2.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: invalid use of void expression ```text [ 77%] Linking CXX executable tutorial/11_read_mapper/read_mapper_step2_snippet In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-printers.h:110, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-matchers.h:44, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/internal/gtest-death-test-internal.h:39, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-death-test.h:41, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:64: /usr/include/c++/12/utility:108:10: note: declared here 108 | void as_const(const _Tp&&) = delete; ```
Error 13: error: invalid use of void expression ```text [ 77%] Building CXX object CMakeFiles/sam_flags_snippet.dir/io/sam_file/sam_flags.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7860: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 14: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/structure_file_input_structured_bindings_snippet.dir/io/structure_file/structure_file_input_structured_bindings.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), ```
Error 15: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3453557336 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 23%] Building CXX object alignment/pairwise/edit_distance/CMakeFiles/global_edit_distance_unbanded_test.dir/global_edit_distance_unbanded_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 44%] Building CXX object alphabet/views/CMakeFiles/translate_join_test.dir/translate_join_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: ```
Error 6: error: invalid use of void expression ```text [ 48%] Building CXX object argument_parser/detail/CMakeFiles/concept_is_container_option_test.dir/concept_is_container_option_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_cout_write_snippet.dir/io/sam_file/sam_file_output_cout_write.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ ```
Error 10: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_filename_construction_snippet.dir/io/sam_file/sam_file_output_filename_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:630:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:370:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:835:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 835 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:836:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 836 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:856:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 856 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:857:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 857 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:86: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 11: error: no match for ‘operator<<’ ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 12: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_filename_construction_with_ref_info_snippet.dir/io/sam_file/sam_file_output_filename_construction_with_ref_info.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits<>; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:630:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits<>; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:572:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:835:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 835 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:836:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 836 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:856:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 856 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:857:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 857 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:86: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 13: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:391:10: note: declared here 391 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ ```
Error 14: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7860: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 15: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 76%] Building CXX object CMakeFiles/structure_file_output_push_back_snippet.dir/io/structure_file/structure_file_output_push_back.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 16: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3453557336 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 39%] Building CXX object alphabet/nucleotide/CMakeFiles/nucleotide_conversion_integration_test.dir/nucleotide_conversion_integration_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 2; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 1, std::vector > >’ ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 46%] Building CXX object argument_parser/detail/CMakeFiles/format_man_test.dir/format_man_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 80%] Building CXX object CMakeFiles/align_cfg_output_begin_position_snippet.dir/alignment/configuration/align_cfg_output_begin_position.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 80%] Building CXX object CMakeFiles/sequence_file_output_view_pipeline_snippet.dir/io/sequence_file/sequence_file_output_view_pipeline.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_filter_criteria_snippet.dir/io/structure_file/structure_file_input_filter_criteria.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 13: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 81%] Building CXX object CMakeFiles/solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/02_argument_parser/solution4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 14: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_move_snippet.dir/io/structure_file/structure_file_input_move.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:83: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: ```
Error 15: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_record_iter_snippet.dir/io/structure_file/structure_file_input_record_iter.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:55: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 16: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_mod_traits_snippet.dir/io/structure_file/structure_file_input_mod_traits.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 17: error: forming reference to void ```text [ 68%] Building CXX object io/sequence_file/CMakeFiles/sequence_file_format_fastq_test.dir/sequence_file_format_fastq_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade becau
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3506175909 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 23%] Building CXX object alignment/pairwise/edit_distance/CMakeFiles/global_edit_distance_unbanded_test.dir/global_edit_distance_unbanded_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: ```
Error 6: error: invalid use of void expression ```text [ 47%] Building CXX object argument_parser/detail/CMakeFiles/format_help_test.dir/format_help_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 62%] Building CXX object io/detail/CMakeFiles/misc_output_test.dir/misc_output_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_format_construction_snippet.dir/io/sam_file/sam_file_output_format_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 76%] Building CXX object CMakeFiles/structure_file_output_push_back_snippet.dir/io/structure_file/structure_file_output_push_back.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 13: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 77%] Building CXX object CMakeFiles/read_mapper_step2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step2.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 14: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:391:10: note: declared here 391 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ ```
Error 15: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7860: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 16: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 65%] Building CXX object io/sam_file/CMakeFiles/sam_file_input_test.dir/sam_file_input_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3506175909 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: ```
Error 6: error: invalid use of void expression ```text [ 46%] Building CXX object argument_parser/detail/CMakeFiles/format_man_test.dir/format_man_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 48%] Building CXX object argument_parser/detail/CMakeFiles/version_check_debug_test.dir/version_check_debug_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 58%] Building CXX object core/range/CMakeFiles/range_iterator_test.dir/range_iterator_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 77%] Building CXX object CMakeFiles/minimisers_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/minimisers_solution3.cpp.o /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 13: error: invalid use of void expression ```text [ 77%] Building CXX object CMakeFiles/sam_flags_snippet.dir/io/sam_file/sam_flags.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-printers.h:110, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-matchers.h:44, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/internal/gtest-death-test-internal.h:39, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-death-test.h:41, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:64: /usr/include/c++/12/utility:108:10: note: declared here 108 | void as_const(const _Tp&&) = delete; ```
Error 14: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7860: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 15: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/structure_file_input_structured_bindings_snippet.dir/io/structure_file/structure_file_input_structured_bindings.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), ```
Error 16: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3506175909 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 21%] Building CXX object alignment/pairwise/CMakeFiles/global_affine_unbanded_test.dir/global_affine_unbanded_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 37%] Building CXX object alphabet/nucleotide/CMakeFiles/dna5_test.dir/dna5_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 2; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 1, std::vector > >’ ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 75%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 80%] Building CXX object CMakeFiles/customisation_point_snippet.dir/core/detail/customisation_point.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_filter_criteria_snippet.dir/io/structure_file/structure_file_input_filter_criteria.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:630:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:370:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:835:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 835 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:836:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 836 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:856:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 856 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:857:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 857 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:86: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 12: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 81%] Building CXX object CMakeFiles/solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/02_argument_parser/solution4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 13: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_move_snippet.dir/io/structure_file/structure_file_input_move.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 14: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_record_iter_snippet.dir/io/structure_file/structure_file_input_record_iter.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 15: error: inline function ‘bool seqan3::operator< ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_ref_return_snippet.dir/io/structure_file/structure_file_input_ref_return.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp: At global scope: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp:487:17: error: inline function ‘bool seqan3::operator<(const seqan3::gap_decorator, false> >&, const seqan3::gap_decorator, false> >&)’ used but never defined [-Werror] 487 | friend bool operator<(gap_decorator const & lhs, gap_decorator const & rhs) | ^~~~~~~~ cc1plus: all warnings being treated as errors gmake[5]: *** [io/sam_file/CMakeFiles/format_bam_test.dir/build.make:66: io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/format_bam_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7804: io/sam_file/CMakeFiles/format_bam_test.dir/all] Error 2 Scanning dependencies of target sam_file_record_test ```
Error 16: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:83: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: ```
Error 17: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_skip_fields_snippet.dir/io/structure_file/structure_file_input_skip_fields.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:55: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-bu
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3556378528 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 60%] Building CXX object io/detail/CMakeFiles/record_like_test.dir/record_like_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 76%] Building CXX object CMakeFiles/list_traits_take_snippet.dir/utility/type_list/list_traits_take.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ ```
Error 11: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 77%] Building CXX object CMakeFiles/sam_file_output_write_range_snippet.dir/io/sam_file/sam_file_output_write_range.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:630:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:370:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:835:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 835 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:836:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 836 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:856:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 856 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:857:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 857 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:86: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 12: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 13: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:391:10: note: declared here 391 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ ```
Error 14: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7860: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 15: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 65%] Building CXX object io/sam_file/CMakeFiles/sam_file_input_test.dir/sam_file_input_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 16: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 77%] Building CXX object CMakeFiles/minimisers_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/minimisers_solution3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits >, const std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:704:13: required from ‘seqan3::sam_file_input::header_type& seqan3::sam_file_input::header() [with traits_type_ = seqan3::sam_file_input_default_traits >, const std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::header_type = seqan3::sam_file_header > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:541:5: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:835:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 835 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:836:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 836 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:856:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 856 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:857:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 857 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/inclu
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3556378528 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 48%] Building CXX object argument_parser/detail/CMakeFiles/concept_is_container_option_test.dir/concept_is_container_option_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 58%] Building CXX object core/range/CMakeFiles/range_iterator_test.dir/range_iterator_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 77%] Building CXX object CMakeFiles/minimisers_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/minimisers_solution3.cpp.o /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 13: error: invalid use of void expression ```text [ 77%] Building CXX object CMakeFiles/sam_flags_snippet.dir/io/sam_file/sam_flags.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-printers.h:110, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-matchers.h:44, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/internal/gtest-death-test-internal.h:39, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-death-test.h:41, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:64: /usr/include/c++/12/utility:108:10: note: declared here 108 | void as_const(const _Tp&&) = delete; ```
Error 14: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 15: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 65%] Building CXX object io/sam_file/CMakeFiles/sam_file_input_test.dir/sam_file_input_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), ```
Error 16: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3556378528 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 21%] Building CXX object alignment/pairwise/CMakeFiles/global_affine_unbanded_test.dir/global_affine_unbanded_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 37%] Building CXX object alphabet/nucleotide/CMakeFiles/dna5_test.dir/dna5_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 2; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 1, std::vector > >’ ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 75%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_filter_criteria_snippet.dir/io/structure_file/structure_file_input_filter_criteria.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 81%] Building CXX object CMakeFiles/solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/02_argument_parser/solution4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_move_snippet.dir/io/structure_file/structure_file_input_move.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 13: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 81%] Building CXX object CMakeFiles/simd_traits_snippet.dir/utility/simd/simd_traits.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 14: error: inline function ‘bool seqan3::operator< ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_ref_return_snippet.dir/io/structure_file/structure_file_input_ref_return.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp: At global scope: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp:487:17: error: inline function ‘bool seqan3::operator<(const seqan3::gap_decorator, false> >&, const seqan3::gap_decorator, false> >&)’ used but never defined [-Werror] 487 | friend bool operator<(gap_decorator const & lhs, gap_decorator const & rhs) | ^~~~~~~~ cc1plus: all warnings being treated as errors gmake[5]: *** [io/sam_file/CMakeFiles/format_bam_test.dir/build.make:66: io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/format_bam_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7804: io/sam_file/CMakeFiles/format_bam_test.dir/all] Error 2 Scanning dependencies of target sam_file_record_test ```
Error 15: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/dynamic_bitset_set_all_snippet.dir/utility/container/dynamic_bitset_set_all.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:83: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: ```
Error 16: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_skip_fields_snippet.dir/io/structure_file/structure_file_input_skip_fields.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:55: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 17: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 84%] Building CXX object CMakeFiles/counting_agent_construction_snippet.dir/search/dream_index/counting_agent_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3611261939 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 58%] Building CXX object core/range/CMakeFiles/range_iterator_test.dir/range_iterator_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 77%] Building CXX object CMakeFiles/minimisers_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/minimisers_solution3.cpp.o /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 13: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-printers.h:110, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-matchers.h:44, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/internal/gtest-death-test-internal.h:39, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-death-test.h:41, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:64: /usr/include/c++/12/utility:108:10: note: declared here 108 | void as_const(const _Tp&&) = delete; ```
Error 14: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 15: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 65%] Building CXX object io/sam_file/CMakeFiles/sam_file_input_test.dir/sam_file_input_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), ```
Error 16: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3611261939 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 59%] Building CXX object io/detail/CMakeFiles/ignore_output_iterator_test.dir/ignore_output_iterator_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/read_mapper_step2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step2.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ ```
Error 11: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:391:10: note: declared here 391 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ ```
Error 13: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 14: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/sam_flags_snippet.dir/io/sam_file/sam_flags.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 15: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ ```
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3611261939 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 39%] Building CXX object alphabet/nucleotide/CMakeFiles/nucleotide_conversion_integration_test.dir/nucleotide_conversion_integration_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 2; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 1, std::vector > >’ ```
Error 6: error: invalid use of void expression ```text [ 43%] Building CXX object alphabet/views/CMakeFiles/char_strictly_to_test.dir/char_strictly_to_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 47%] Building CXX object argument_parser/detail/CMakeFiles/format_help_test.dir/format_help_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 79%] Building CXX object CMakeFiles/sequence_file_output_col_based_writing_snippet.dir/io/sequence_file/sequence_file_output_col_based_writing.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 80%] Building CXX object CMakeFiles/bloom_filter_reset_snippet.dir/utility/bloom_filter/bloom_filter_reset.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 80%] Building CXX object CMakeFiles/sequence_file_output_template_deduction_snippet.dir/io/sequence_file/sequence_file_output_template_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 13: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 80%] Linking CXX executable tutorial/07_sequence_file/sequence_file_piping_in_out_snippet In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:244:32: required from ‘void gtest_suite_sam_file_read_::read_in_alignment_only_with_ref::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:240:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:244:32: required from ‘void gtest_suite_sam_file_read_::read_in_alignment_only_with_ref::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ ```
Error 14: error: no match for ‘operator*’ ```text [ 80%] Built target sequence_file_piping_in_out_snippet In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_read_::read_in_alignment_only_with_ref::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:240:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:251:9: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >’}) 251 | for (auto & [alignment] : fin) | ^~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:267:53: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >’}) 267 | EXPECT_TRUE(std::ranges::empty(std::get<0>((*fin.begin()).alignment()))); | ~^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:268:53: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >’}) 268 | EXPECT_TRUE(std::ranges::empty(std::get<1>((*fin.begin()).alignment()))); | ~^~~~~~~~~~~~~ Scanning dependencies of target sequence_file_output_view_pipeline_snippet ```
Error 15: error: invalid use of void expression ```text [ 80%] Building CXX object CMakeFiles/sequence_file_output_view_pipeline_snippet.dir/io/sequence_file/sequence_file_output_view_pipeline.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_read_::read_in_all_but_empty_data::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:209:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:220:72: error: invalid use of void expression 220 | EXPECT_TRUE(std::ranges::empty(std::get<0>((*fin.begin()).alignment()))); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:221:72: error: invalid use of void expression 221 | EXPECT_TRUE(std::ranges::empty(std::get<1>((*fin.begin()).alignment()))); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_read_::read_in_all_data::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:167:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:197:50: error: invalid use of void expression 197 | EXPECT_RANGE_EQ(std::get<0>(rec.alignment()), std::get<0>(this->alignments[i])); | ~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:197:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 197 | EXPECT_RANGE_EQ(std::get<0>(rec.alignment()), std::get<0>(this->alignments[i])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:198:50: error: invalid use of void expression 198 | EXPECT_RANGE_EQ(std::get<1>(rec.alignment()), std::get<1>(this->alignments[i])); | ~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:198:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 198 | EXPECT_RANGE_EQ(std::get<1>(rec.alignment()), std::get<1>(this->alignments[i])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_read_::read_in_alignment_only_without_ref::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:272:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:279:9: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator, seqan3::fields, seqan3::type_list > >’}) 279 | for (auto & [alignment] : fin) ```
Error 16: error: inline function ‘bool seqan3::operator< ```text [ 80%] Building CXX object CMakeFiles/structure_file_input_data_out_snippet.dir/io/structure_file/structure_file_input_data_out.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp: At global scope: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp:487:17: error: inline function ‘bool seqan3::operator<(const seqan3::gap_decorator, false> >&, const seqan3::gap_decorator, false> >&)’ used but never defined [-Werror] 487 | friend bool operator<(gap_decorator const & lhs, gap_decorator const & rhs) | ^~~~~~~~ cc1plus: all warnings being treated as errors gmake[5]: *** [io/sam_file/CMakeFiles/format_bam_test.dir/build.make:66: io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/format_bam_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7804: io/sam_file/CMakeFiles/format_bam_test.dir/all] Error 2 Scanning dependencies of target sam_file_record_test ```
Error 17: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:83: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3666974996 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Linking CXX executable tutorial/10_sam_file/sam_file_read_cigar_snippet /usr/include/c++/11/bits/ranges_base.h:577:20: note: the required expression ‘std::ranges::__cust::end(__t)’ is invalid 577 | ranges::end(__t); | ~~~~~~~~~~~^~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate expects 1 argument, 4 provided In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:329:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >, int, int, bool)’ 329 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref, read), 5, 60, true)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: constraints not satisfied In file included from /usr/include/c++/11/string_view:48, from /usr/include/c++/11/bits/basic_string.h:48, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, ```
Error 4: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator&>]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair&>, seqan3::gap_decorator&> >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair&>, seqan3::gap_decorator&> >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair&>, seqan3::gap_decorator&> >)’ ```
Error 5: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 6: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 7: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: ```
Error 8: error: invalid use of void expression ```text [ 47%] Building CXX object argument_parser/detail/CMakeFiles/version_check_release_test.dir/version_check_release_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 9: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_cout_write_snippet.dir/io/sam_file/sam_file_output_cout_write.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 11: error: no match for ‘operator<<’ ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 12: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_filename_construction_with_ref_info_snippet.dir/io/sam_file/sam_file_output_filename_construction_with_ref_info.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:630:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:370:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:835:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 835 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:836:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 836 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:856:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 856 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:857:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 857 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:86: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 13: error: invalid use of void expression ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_io_pipeline_snippet.dir/io/sam_file/sam_file_output_io_pipeline.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 14: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:391:10: note: declared here 391 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ ```
Error 15: error: invalid use of void expression ```text [ 77%] Building CXX object CMakeFiles/sam_file_output_write_range_snippet.dir/io/sam_file/sam_file_output_write_range.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7860: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 16: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/read_mapper_step2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step2.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11:
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3666974996 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 48%] Building CXX object argument_parser/detail/CMakeFiles/version_check_debug_test.dir/version_check_debug_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 58%] Building CXX object core/range/detail/CMakeFiles/random_access_iterator_test.dir/random_access_iterator_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: invalid use of void expression ```text [ 77%] Linking CXX executable tutorial/06_minimisers/minimisers_solution3_snippet In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ ```
Error 13: error: use of deleted function ‘void std::as_const ```text [ 77%] Built target minimisers_solution3_snippet /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-printers.h:110, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-matchers.h:44, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/internal/gtest-death-test-internal.h:39, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-death-test.h:41, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:64: /usr/include/c++/12/utility:108:10: note: declared here 108 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) ```
Error 14: error: use of deleted function ‘void std::as_const ```text [ 77%] Building CXX object CMakeFiles/sam_flags_snippet.dir/io/sam_file/sam_flags.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:254:72: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 254 | EXPECT_SAME_TYPE(int32_t const &&, decltype(std::move(std::as_const(r.sequence_position())))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:254:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 254 | EXPECT_SAME_TYPE(int32_t const &&, decltype(std::move(std::as_const(r.sequence_position())))); | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/utility:108:10: note: declared here 108 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:254:72: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 254 | EXPECT_SAME_TYPE(int32_t const &&, decltype(std::move(std::as_const(r.sequence_position())))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); ```
Error 15: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7860: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 16: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/structure_file_input_structured_bindings_snippet.dir/io/structure_file/structure_file_input_structured_bindings.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), ```
Error 17: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3666974996 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 39%] Building CXX object alphabet/nucleotide/CMakeFiles/nucleotide_conversion_integration_test.dir/nucleotide_conversion_integration_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 2; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 1, std::vector > >’ ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 47%] Building CXX object argument_parser/detail/CMakeFiles/format_help_test.dir/format_help_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 79%] Building CXX object CMakeFiles/sequence_file_output_col_based_writing_snippet.dir/io/sequence_file/sequence_file_output_col_based_writing.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 80%] Building CXX object CMakeFiles/bloom_filter_reset_snippet.dir/utility/bloom_filter/bloom_filter_reset.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 80%] Building CXX object CMakeFiles/sequence_file_output_template_deduction_snippet.dir/io/sequence_file/sequence_file_output_template_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 13: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 80%] Building CXX object CMakeFiles/sequence_file_output_view_pipeline_snippet.dir/io/sequence_file/sequence_file_output_view_pipeline.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 14: error: inline function ‘bool seqan3::operator< ```text [ 80%] Building CXX object CMakeFiles/structure_file_input_data_out_snippet.dir/io/structure_file/structure_file_input_data_out.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp: At global scope: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp:487:17: error: inline function ‘bool seqan3::operator<(const seqan3::gap_decorator, false> >&, const seqan3::gap_decorator, false> >&)’ used but never defined [-Werror] 487 | friend bool operator<(gap_decorator const & lhs, gap_decorator const & rhs) | ^~~~~~~~ cc1plus: all warnings being treated as errors gmake[5]: *** [io/sam_file/CMakeFiles/format_bam_test.dir/build.make:66: io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/format_bam_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7804: io/sam_file/CMakeFiles/format_bam_test.dir/all] Error 2 Scanning dependencies of target sam_file_record_test ```
Error 15: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:83: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: ```
Error 16: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_filter_criteria_snippet.dir/io/structure_file/structure_file_input_filter_criteria.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:55: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 17: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_move_snippet.dir/io/structure_file/structure_file_input_move.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 18: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_record_iter_snippet.dir/io/structure_fil
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3722798673 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 60%] Building CXX object io/detail/CMakeFiles/record_like_test.dir/record_like_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/sam_file_output_write_range_snippet.dir/io/sam_file/sam_file_output_write_range.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ ```
Error 11: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:391:10: note: declared here 391 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ ```
Error 13: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7860: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 14: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 65%] Building CXX object io/sam_file/CMakeFiles/sam_file_input_test.dir/sam_file_input_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 15: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 77%] Building CXX object CMakeFiles/minimisers_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/minimisers_solution3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits >, const std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:704:13: required from ‘seqan3::sam_file_input::header_type& seqan3::sam_file_input::header() [with traits_type_ = seqan3::sam_file_input_default_traits >, const std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::header_type = seqan3::sam_file_header > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:541:5: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:835:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 835 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:836:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 836 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:856:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 856 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:857:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 857 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:86: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:862:81: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ ```
Error 16: error: forming reference to void ```text [ 73%] Building CXX object search/CMakeFiles/search_scheme_test.dir/search_scheme_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3722798673 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 58%] Building CXX object core/range/CMakeFiles/range_iterator_test.dir/range_iterator_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 77%] Building CXX object CMakeFiles/minimisers_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/minimisers_solution3.cpp.o /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 13: error: invalid use of void expression ```text [ 77%] Building CXX object CMakeFiles/sam_flags_snippet.dir/io/sam_file/sam_flags.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_read_::read_in_all_but_empty_data::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:209:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:220:72: error: invalid use of void expression 220 | EXPECT_TRUE(std::ranges::empty(std::get<0>((*fin.begin()).alignment()))); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:221:72: error: invalid use of void expression 221 | EXPECT_TRUE(std::ranges::empty(std::get<1>((*fin.begin()).alignment()))); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_read_::read_in_all_data::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:167:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:197:50: error: invalid use of void expression 197 | EXPECT_RANGE_EQ(std::get<0>(rec.alignment()), std::get<0>(this->alignments[i])); | ~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:197:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 197 | EXPECT_RANGE_EQ(std::get<0>(rec.alignment()), std::get<0>(this->alignments[i])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:198:50: error: invalid use of void expression 198 | EXPECT_RANGE_EQ(std::get<1>(rec.alignment()), std::get<1>(this->alignments[i])); | ~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:198:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 198 | EXPECT_RANGE_EQ(std::get<1>(rec.alignment()), std::get<1>(this->alignments[i])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_read_::read_in_alignment_only_without_ref::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:272:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:279:9: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator, seqan3::fields, seqan3::type_list > >’}) 279 | for (auto & [alignment] : fin) | ^~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:291:53: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator, seqan3::fields, seqan3::type_list > >’}) 291 | EXPECT_TRUE(std::ranges::empty(std::get<0>((*fin.begin()).alignment()))); ```
Error 14: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-printers.h:110, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-matchers.h:44, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/internal/gtest-death-test-internal.h:39, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-death-test.h:41, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:64: /usr/include/c++/12/utility:108:10: note: declared here 108 | void as_const(const _Tp&&) = delete; ```
Error 15: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 16: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Linking CXX executable io/structure_file/structure_file_input_structured_bindings_snippet In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::_
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3722798673 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 39%] Building CXX object alphabet/nucleotide/CMakeFiles/rna15_test.dir/rna15_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 2; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 1, std::vector > >’ ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 75%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 80%] Building CXX object CMakeFiles/bloom_filter_reset_snippet.dir/utility/bloom_filter/bloom_filter_reset.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 80%] Built target sequence_file_piping_in_out_snippet Scanning dependencies of target sequence_file_output_view_pipeline_snippet In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], ```
Error 12: error: no match for ‘operator*’ ```text [ 80%] Building CXX object CMakeFiles/sequence_file_output_view_pipeline_snippet.dir/io/sequence_file/sequence_file_output_view_pipeline.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_read_::read_in_alignment_only_with_ref::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:240:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:251:9: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >’}) 251 | for (auto & [alignment] : fin) | ^~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:267:53: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >’}) 267 | EXPECT_TRUE(std::ranges::empty(std::get<0>((*fin.begin()).alignment()))); | ~^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:268:53: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >’}) 268 | EXPECT_TRUE(std::ranges::empty(std::get<1>((*fin.begin()).alignment()))); | ~^~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:566:33: required from ‘void gtest_suite_sam_file_write_::with_header::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:539:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { ```
Error 13: error: invalid use of void expression ```text [ 80%] Building CXX object CMakeFiles/structure_file_input_data_out_snippet.dir/io/structure_file/structure_file_input_data_out.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 14: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 80%] Building CXX object CMakeFiles/dna15_implicit_conversion_from_rna15_views_snippet.dir/alphabet/nucleotide/dna15_implicit_conversion_from_rna15_views.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits<>; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:630:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits<>; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:572:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:835:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 835 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:836:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 836 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:856:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 856 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:857:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 857 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:86: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 15: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_filter_criteria_snippet.dir/io/structure_file/structure_file_input_filter_criteria.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 16: error: inline function ‘bool seqan3::operator< ```text [ 81%] Building CXX object CMakeFiles/solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/02_argument_parser/solution4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp: At global scope: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp:487:17: error: inline function ‘bool seqan3::operator<(const seqan3::gap_decorator, false> >&, const seqan3::gap_decorator, false> >&)’ used but never defined [-Werror] 487 | friend bool operator<(gap_decorator const & lhs, gap_decorator const & rhs) | ^~~~~~~~ cc1plus: all warnings being treated as errors gmake[5]: *** [io/sam_file/CMakeFiles/format_bam_test.dir/build.make:66: io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/format_bam_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7804: io/sam_file/CMakeFiles/format_bam_test.dir/all] Error 2 Scanning dependencies of target sam_file_record_test ```
Error 17: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:83: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3773898940 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 23%] Building CXX object alignment/pairwise/edit_distance/CMakeFiles/global_edit_distance_unbanded_test.dir/global_edit_distance_unbanded_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 61%] Building CXX object io/detail/CMakeFiles/misc_test.dir/misc_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_io_pipeline_snippet.dir/io/sam_file/sam_file_output_io_pipeline.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 77%] Built target list_traits_take_snippet In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 77%] Building CXX object CMakeFiles/sam_file_output_write_range_snippet.dir/io/sam_file/sam_file_output_write_range.cpp.o /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:646:33: required from ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_read_::read_in_alignment_only_with_ref::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:240:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:251:9: error: no match for ‘operator*’ (operand type is ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::iterator’ {aka ‘seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >’}) 251 | for (auto & [alignment] : fin) | ^~~ ```
Error 13: error: invalid use of void expression ```text [ 77%] Building CXX object CMakeFiles/read_mapper_step2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step2.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 14: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:391:10: note: declared here 391 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ ```
Error 15: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_seek_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_seek_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7860: io/sam_file/CMakeFiles/sam_file_seek_test.dir/all] Error 2 Scanning dependencies of target sam_file_input_test ```
Error 16: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 65%] Building CXX object io/sam_file/CMakeFiles/sam_file_input_test.dir/sam_file_input_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3773898940 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 58%] Building CXX object core/range/CMakeFiles/range_iterator_test.dir/range_iterator_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 77%] Building CXX object CMakeFiles/minimisers_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/minimisers_solution3.cpp.o /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 13: error: invalid use of void expression ```text [ 77%] Building CXX object CMakeFiles/sam_flags_snippet.dir/io/sam_file/sam_flags.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-printers.h:110, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-matchers.h:44, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/internal/gtest-death-test-internal.h:39, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-death-test.h:41, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:64: /usr/include/c++/12/utility:108:10: note: declared here 108 | void as_const(const _Tp&&) = delete; ```
Error 14: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 15: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 65%] Building CXX object io/sam_file/CMakeFiles/sam_file_input_test.dir/sam_file_input_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), ```
Error 16: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3773898940 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 39%] Building CXX object alphabet/nucleotide/CMakeFiles/rna5_test.dir/rna5_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 2; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 1, std::vector > >’ ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 75%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 80%] Building CXX object CMakeFiles/sequence_file_output_template_deduction_snippet.dir/io/sequence_file/sequence_file_output_template_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 80%] Building CXX object CMakeFiles/sequence_file_output_view_pipeline_snippet.dir/io/sequence_file/sequence_file_output_view_pipeline.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 80%] Building CXX object CMakeFiles/structure_file_input_data_out_snippet.dir/io/structure_file/structure_file_input_data_out.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/02_argument_parser/solution4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 13: error: inline function ‘bool seqan3::operator< ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_move_snippet.dir/io/structure_file/structure_file_input_move.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp: At global scope: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp:487:17: error: inline function ‘bool seqan3::operator<(const seqan3::gap_decorator, false> >&, const seqan3::gap_decorator, false> >&)’ used but never defined [-Werror] 487 | friend bool operator<(gap_decorator const & lhs, gap_decorator const & rhs) | ^~~~~~~~ cc1plus: all warnings being treated as errors gmake[5]: *** [io/sam_file/CMakeFiles/format_bam_test.dir/build.make:66: io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/format_bam_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7804: io/sam_file/CMakeFiles/format_bam_test.dir/all] Error 2 Scanning dependencies of target sam_file_record_test ```
Error 14: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_record_iter_snippet.dir/io/structure_file/structure_file_input_record_iter.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:83: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: ```
Error 15: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_ref_return_snippet.dir/io/structure_file/structure_file_input_ref_return.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:55: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 16: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_skip_fields_snippet.dir/io/structure_file/structure_file_input_skip_fields.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 17: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ ```
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3814787806 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 58%] Building CXX object core/detail/CMakeFiles/transfer_type_modifier_onto_test.dir/transfer_type_modifier_onto_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/format_sam_test.dir/format_sam_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: invalid use of void expression ```text [ 77%] Building CXX object CMakeFiles/minimisers_solution3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/minimisers_solution3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 77%] Building CXX object CMakeFiles/sam_flags_snippet.dir/io/sam_file/sam_flags.cpp.o /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 13: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-printers.h:110, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-matchers.h:44, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/internal/gtest-death-test-internal.h:39, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest-death-test.h:41, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:64: /usr/include/c++/12/utility:108:10: note: declared here 108 | void as_const(const _Tp&&) = delete; ```
Error 14: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 15: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/general_usage_snippet.dir/io/sam_file/sam_tag_dictionary/general_usage.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), ```
Error 16: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3814787806 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 23%] Building CXX object alignment/pairwise/edit_distance/CMakeFiles/global_edit_distance_unbanded_test.dir/global_edit_distance_unbanded_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 43%] Building CXX object alphabet/views/CMakeFiles/rank_to_test.dir/rank_to_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 54%] Building CXX object core/algorithm/detail/CMakeFiles/algorithm_executor_blocking_test.dir/algorithm_executor_blocking_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_filename_construction_snippet.dir/io/sam_file/sam_file_output_filename_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ ```
Error 10: error: using invalid field ‘seqan3::sam_file_input<traits_type_, selected_field_ids_, valid_formats_>::record_ ```text [ 75%] Built target sam_file_output_filename_construction_snippet In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘void seqan3::sam_file_input::read_next_record() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list]’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:630:13: required from ‘seqan3::sam_file_input::iterator seqan3::sam_file_input::begin() [with traits_type_ = seqan3::sam_file_input_default_traits >, std::vector > >; selected_field_ids_ = seqan3::fields; valid_formats_ = seqan3::type_list; seqan3::sam_file_input::iterator = seqan3::detail::in_file_iterator >, std::vector > >, seqan3::fields, seqan3::type_list > >]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:370:9: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:835:9: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 835 | record_buffer.clear(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:836:50: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 836 | detail::get_or_ignore(record_buffer) = header_ptr.get(); | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:856:79: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 856 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:857:80: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 857 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:858:78: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 858 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:859:83: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 859 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:860:82: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 860 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:861:86: error: using invalid field ‘seqan3::sam_file_input::record_buffer’ 861 | detail::get_or_ignore(record_buffer), | ^~~~~~~~~~~~~ ```
Error 11: error: no match for ‘operator<<’ ```text [ 75%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 12: error: invalid use of void expression ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_filename_construction_with_ref_info_snippet.dir/io/sam_file/sam_file_output_filename_construction_with_ref_info.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 13: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_format_construction_snippet.dir/io/sam_file/sam_file_output_format_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 14: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:391:10: note: declared here 391 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ ```
Error 15: error: invalid use of void expression ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:25: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 16: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 77%] Building CXX object CMakeFiles/sam_file_output_write_range_snippet.dir/io/sam_file/sam_file_output_write_range.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3814787806 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/sam_file_read_cigar_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_read_cigar.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:128:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 128 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 173 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:173:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 37%] Building CXX object alphabet/nucleotide/CMakeFiles/dna4_test.dir/dna4_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 2; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 1, std::vector > >’ ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 75%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_filter_criteria_snippet.dir/io/structure_file/structure_file_input_filter_criteria.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 81%] Building CXX object CMakeFiles/solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/02_argument_parser/solution4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_move_snippet.dir/io/structure_file/structure_file_input_move.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 13: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_record_iter_snippet.dir/io/structure_file/structure_file_input_record_iter.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 14: error: inline function ‘bool seqan3::operator< ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_ref_return_snippet.dir/io/structure_file/structure_file_input_ref_return.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp: At global scope: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alignment/decorator/gap_decorator.hpp:487:17: error: inline function ‘bool seqan3::operator<(const seqan3::gap_decorator, false> >&, const seqan3::gap_decorator, false> >&)’ used but never defined [-Werror] 487 | friend bool operator<(gap_decorator const & lhs, gap_decorator const & rhs) | ^~~~~~~~ cc1plus: all warnings being treated as errors gmake[5]: *** [io/sam_file/CMakeFiles/format_bam_test.dir/build.make:66: io/sam_file/CMakeFiles/format_bam_test.dir/format_bam_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/format_bam_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7804: io/sam_file/CMakeFiles/format_bam_test.dir/all] Error 2 Scanning dependencies of target sam_file_record_test ```
Error 15: error: invalid use of void expression ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:83: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: ```
Error 16: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_skip_fields_snippet.dir/io/structure_file/structure_file_input_skip_fields.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp: In instantiation of ‘static void sam_file_seek_test::expect_record_eq(record_t&, expected_record_t&) [with record_t = seqan3::sam_record >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields >; expected_record_t = seqan3::sam_record, std::allocator >, std::vector >, std::vector >, int, std::pair, std::allocator > >, std::vector, std::allocator > > >, std::optional, std::optional, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*, seqan3::sam_flag, std::tuple, std::optional, int>, unsigned char, std::vector >, seqan3::sam_tag_dictionary>, seqan3::fields >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:71:55: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:53: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:95: error: invalid use of void expression 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:44:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 44 | EXPECT_RANGE_EQ(std::get<1>(record.alignment()), std::get<1>(expected_record.alignment())); | ^~~~~~~~~~~~~~~ ```
Error 17: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 84%] Building CXX object CMakeFiles/counting_agent_construction_snippet.dir/search/dream_index/counting_agent_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_sta
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/3864977805 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 166 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/sam_file_filename_construction_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_filename_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 166 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 44%] Building CXX object alphabet/views/CMakeFiles/translate_join_test.dir/translate_join_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::{}.seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_filename_construction_snippet.dir/io/sam_file/sam_file_output_filename_construction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ ```
Error 10: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 75%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 11: error: invalid use of void expression ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_filename_construction_with_ref_info_snippet.dir/io/sam_file/sam_file_output_filename_construction_with_ref_info.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 12: error: no matching function for call to ‘get<0> ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:26: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp: In function ‘std::vector seqan3::test::operator""_cigar(const char*, std::size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: error: no matching function for call to ‘get<0>(std::vector)’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:223:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(std::pair<_Tp1, _Tp2>&)’ 223 | get(pair<_Tp1, _Tp2>& __in) noexcept | ^~~ /usr/include/c++/11/utility:223:5: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:26: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: note: ‘std::vector’ is not derived from ‘std::pair<_Tp1, _Tp2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:228:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(std::pair<_Tp1, _Tp2>&&)’ 228 | get(pair<_Tp1, _Tp2>&& __in) noexcept | ^~~ /usr/include/c++/11/utility:228:5: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:26: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: note: ‘std::vector’ is not derived from ‘std::pair<_Tp1, _Tp2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 13: error: invalid use of void expression ```text [ 75%] Building CXX object CMakeFiles/sam_file_output_io_pipeline_snippet.dir/io/sam_file/sam_file_output_io_pipeline.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:61: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/11/utility:391:10: note: declared here 391 | void as_const(const _Tp&&) = delete; | ^~~~~~~~ ```
Error 14: error: no matching function for call to ‘get<0> ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/fixture/io/sam_file/simple_three_verbose_reads_fixture.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp: In function ‘std::vector seqan3::test::operator""_cigar(const char*, std::size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: error: no matching function for call to ‘get<0>(std::vector)’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /usr/include/c++/11/utility:223:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(std::pair<_Tp1, _Tp2>&)’ 223 | get(pair<_Tp1, _Tp2>& __in) noexcept | ^~~ /usr/include/c++/11/utility:223:5: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/fixture/io/sam_file/simple_three_verbose_reads_fixture.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: note: ‘std::vector’ is not derived from ‘std::pair<_Tp1, _Tp2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/unique_ptr.h:36, from /usr/include/c++/11/memory:76, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /usr/include/c++/11/utility:228:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(std::pair<_Tp1, _Tp2>&&)’ 228 | get(pair<_Tp1, _Tp2>&& __in) noexcept | ^~~ /usr/include/c++/11/utility:228:5: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/fixture/io/sam_file/simple_three_verbose_reads_fixture.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:19: ```
Error 15: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 76%] Building CXX object CMakeFiles/structure_file_output_push_back_snippet.dir/io/structure_file/structure_file_output_push_back.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::{}.seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 16: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/3864977805 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector, seqan3::gap> >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 166 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:78: note: no known conversion for argument 1 from ‘std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >’ to ‘const std::vector&’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair, seqan3::gap> >, std::vector, seqan3::gap> > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 166 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: template argument deduction/substitution failed: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 166 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 166 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: template argument deduction/substitution failed: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 67%] Building CXX object CMakeFiles/sam_file_input_construction_without_automatic_type_deduction_snippet.dir/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:48: note: ‘! seqan3::fields::contains(seqan3::field::offset)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 60%] Building CXX object io/detail/CMakeFiles/in_file_iterator_test.dir/in_file_iterator_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(fmtflags) [with char_t = char; fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 62%] Building CXX object io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: note: ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::().seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::()’ evaluates to false gmake[5]: *** [io/sam_file/CMakeFiles/sam_file_output_test.dir/build.make:66: io/sam_file/CMakeFiles/sam_file_output_test.dir/sam_file_output_test.cpp.o] Error 1 gmake[5]: Target 'io/sam_file/CMakeFiles/sam_file_output_test.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:7748: io/sam_file/CMakeFiles/sam_file_output_test.dir/all] Error 2 Scanning dependencies of target format_sam_test ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 76%] Building CXX object CMakeFiles/list_traits_take_snippet.dir/utility/type_list/list_traits_take.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 77%] Building CXX object CMakeFiles/sam_file_output_write_range_snippet.dir/io/sam_file/sam_file_output_write_range.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ 634 | &(this->header))); ```
Error 12: error: invalid use of void expression ```text [ 77%] Building CXX object CMakeFiles/read_mapper_step2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step2.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) ```
Error 13: error: no matching function for call to ‘get<0> ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:26: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp: In function ‘std::vector seqan3::test::operator""_cigar(const char*, std::size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: error: no matching function for call to ‘get<0>(std::vector)’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:64, from /usr/include/c++/12/memory:63, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/12/bits/stl_pair.h:855:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(pair<_Tp1, _Tp2>&)’ 855 | get(pair<_Tp1, _Tp2>& __in) noexcept | ^~~ /usr/include/c++/12/bits/stl_pair.h:855:5: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: note: ‘std::vector’ is not derived from ‘std::pair<_Tp1, _Tp2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_pair.h:860:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(pair<_Tp1, _Tp2>&&)’ 860 | get(pair<_Tp1, _Tp2>&& __in) noexcept | ^~~ /usr/include/c++/12/bits/stl_pair.h:860:5: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: note: ‘std::vector’ is not derived from ‘std::pair<_Tp1, _Tp2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_pair.h:865:5: note: candidate: ‘template constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(const pair<_Tp1, _Tp2>&)’ 865 | get(const pair<_Tp1, _Tp2>& __in) noexcept | ^~~ /usr/include/c++/12/bits/stl_pair.h:865:5: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: note: ‘std::vector’ is not derived from ‘const std::pair<_Tp1, _Tp2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); ```
Error 14: error: no matching function for call to ‘get<0> ```text [ 64%] Building CXX object io/sam_file/CMakeFiles/sam_file_seek_test.dir/sam_file_seek_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/fixture/io/sam_file/simple_three_verbose_reads_fixture.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp: In function ‘std::vector seqan3::test::operator""_cigar(const char*, std::size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: error: no matching function for call to ‘get<0>(std::vector)’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:64, from /usr/include/c++/12/memory:63, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /usr/include/c++/12/bits/stl_pair.h:855:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(pair<_Tp1, _Tp2>&)’ 855 | get(pair<_Tp1, _Tp2>& __in) noexcept | ^~~ /usr/include/c++/12/bits/stl_pair.h:855:5: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: note: ‘std::vector’ is not derived from ‘std::pair<_Tp1, _Tp2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_pair.h:860:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type&& std::get(pair<_Tp1, _Tp2>&&)’ 860 | get(pair<_Tp1, _Tp2>&& __in) noexcept | ^~~ /usr/include/c++/12/bits/stl_pair.h:860:5: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: note: ‘std::vector’ is not derived from ‘std::pair<_Tp1, _Tp2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_pair.h:865:5: note: candidate: ‘template constexpr const typename std::tuple_element<_Int, std::pair<_Tp1, _Tp2> >::type& std::get(const pair<_Tp1, _Tp2>&)’ 865 | get(const pair<_Tp1, _Tp2>& __in) noexcept | ^~~ /usr/include/c++/12/bits/stl_pair.h:865:5: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:23: note: ‘std::vector’ is not derived from ‘const std::pair<_Tp1, _Tp2>’ ```
Error 15: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 65%] Building CXX object io/sam_file/CMakeFiles/sam_file_input_test.dir/sam_file_input_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:48: note: ‘! seqan3::fields::contains(seqan3::field::alignment)’ evaluates to false /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: note: ‘seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::().seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >::()’ evaluates to false In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. 92 | static_assert(field_types_as_ids::contains(selected_field_ids::as_array[field_no]), ```
Error 16: error: forming reference to void ```text [ 87%] Building CXX object CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp:28:67: error: forming reference to void 28 | auto & [reference_sequence, read_sequence] = record.alignment(); | ^ gmake[5]: *** [CMakeFiles/sam_file_writing_snippet.dir/build.make:66: CMakeFiles/sam_file_writing_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_writing.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_writing_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:14952: CMakeFiles/sam_file_writing_snippet.dir/all] Error 2 Scanning dependencies of target structure_file_input_auto_temp_deduc_snippet ```
github-actions[bot] commented 1 year ago

Failure on gcc10

See https://github.com/seqan/seqan3/actions/runs/3864977805 for more information.

Error 1: error: no matching function for call to ‘get_cigar_string ```text [ 3%] Building CXX object CMakeFiles/read_mapper_indexer_step3_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = std::vector >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:78: note: no known conversion for argument 1 from ‘std::pair >, std::vector > >’ to ‘const std::vector&’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 166 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, std::vector > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/aligned_sequence_test.cpp:15: ```
Error 2: error: no matching function for call to ‘get_cigar_string ```text [ 7%] Building CXX object alignment/decorator/CMakeFiles/gap_decorator_test.dir/gap_decorator_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp: In instantiation of ‘void gtest_suite_aligned_sequence_::cigar_string::TestBody() [with gtest_TypeParam_ = seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > >]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:252:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:34: note: candidate: ‘std::string seqan3::detail::get_cigar_string(const std::vector&)’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:121:78: note: no known conversion for argument 1 from ‘std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >’ to ‘const std::vector&’ 121 | [[nodiscard]] inline std::string get_cigar_string(std::vector const & cigar_vector) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: candidate: ‘template requires (aligned_sequence) && (aligned_sequence) std::string seqan3::detail::get_cigar_string(ref_seq_type&&, query_seq_type&&, uint32_t, uint32_t, bool)’ 166 | [[nodiscard]] inline std::string get_cigar_string(ref_seq_type && ref_seq, | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/detail/cigar.hpp:166:34: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:266:61: note: candidate expects 5 arguments, 1 provided 266 | EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:281:62: error: no matching function for call to ‘get_cigar_string(std::pair >, __gnu_cxx::__normal_iterator > > >, seqan3::gap_decorator >, __gnu_cxx::__normal_iterator > > > >)’ 281 | EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/../../alignment/aligned_sequence_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/alignment/decorator/gap_decorator_test.cpp:19: ```
Error 3: error: invalid use of void expression ```text [ 29%] Building CXX object CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:64:72: error: invalid use of void expression 64 | for (auto const & char_reference : std::get<0>(record.alignment())) | ~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp:69:74: error: invalid use of void expression 69 | size_t sum_read = std::ranges::count(std::get<1>(record.alignment()), seqan3::gap{}); | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_solution2_snippet.dir/build.make:66: CMakeFiles/sam_file_solution2_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_solution2.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_solution2_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5573: CMakeFiles/sam_file_solution2_snippet.dir/all] Error 2 Scanning dependencies of target custom_argument_parsing_enumeration_snippet ```
Error 4: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 31%] Building CXX object CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:10: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp:58:74: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ gmake[5]: *** [CMakeFiles/read_mapper_step4_snippet.dir/build.make:66: CMakeFiles/read_mapper_step4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/11_read_mapper/read_mapper_step4.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/read_mapper_step4_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:5797: CMakeFiles/read_mapper_step4_snippet.dir/all] Error 2 Scanning dependencies of target 3.0.3_literals-namespace_snippet ```
Error 5: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 37%] Building CXX object alphabet/nucleotide/CMakeFiles/dna4_test.dir/dna4_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:32:22: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:368:19: error: static assertion failed: The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front). 368 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/sam_file_input_construction_without_automatic_type_deduction.cpp:3: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 2, std::vector >, std::__cxx11::basic_string, std::allocator > >’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:80:7: required by substitution of ‘template using select_types_with_ids_t = typename seqan3::detail::select_types_with_ids::type [with field_types = seqan3::type_list >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>; field_types_as_ids = seqan3::fields; selected_field_ids = seqan3::fields; long unsigned int field_no = 2; return_types = {std::vector >, std::__cxx11::basic_string, std::allocator >}]’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:96:11: required from ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 1, std::vector > >’ ```
Error 6: error: invalid use of void expression ```text [ 72%] Building CXX object CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp:23:84: error: invalid use of void expression 23 | seqan3::debug_stream << record.id() << ": " << std::get<1>(record.alignment()) << '\n'; | ~~~~~~~~~~~~~~~~^~ gmake[5]: *** [CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build.make:66: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_without_ref.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/sam_file_alignments_without_ref_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12264: CMakeFiles/sam_file_alignments_without_ref_snippet.dir/all] Error 2 Scanning dependencies of target introduction_read_fasta_snippet ```
Error 7: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ ```text [ 75%] Building CXX object CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/snippet/io/sam_file/get_cigar_vector.cpp:41:45: error: ‘get_cigar_vector’ is not a member of ‘seqan3::detail’ 41 | seqan3::debug_stream << seqan3::detail::get_cigar_vector(std::tie(ref, query)) << '\n'; | ^~~~~~~~~~~~~~~~ gmake[5]: *** [CMakeFiles/get_cigar_vector_snippet.dir/build.make:66: CMakeFiles/get_cigar_vector_snippet.dir/io/sam_file/get_cigar_vector.cpp.o] Error 1 gmake[5]: Target 'CMakeFiles/get_cigar_vector_snippet.dir/build' not remade because of errors. gmake[4]: *** [CMakeFiles/Makefile2:12516: CMakeFiles/get_cigar_vector_snippet.dir/all] Error 2 Scanning dependencies of target push_back_record_snippet ```
Error 8: error: no match for ‘operator<<’ ```text [ 75%] Building CXX object CMakeFiles/sam_file_alignments_with_ref_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp: In function ‘int main()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:28:30: error: no match for ‘operator<<’ (operand types are ‘seqan3::debug_stream_type’ and ‘void’) 28 | seqan3::debug_stream << record.alignment() << '\n'; // Now you can print the whole alignment! | ~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~~~~~~~~~~~~ | | | | seqan3::debug_stream_type void In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp:16, from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream.hpp:17, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/test/include/seqan3/test/snippet/create_temporary_snippet_file.hpp:13, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/10_sam_file/sam_file_alignments_with_ref.cpp:1: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(std::ostream& (*)(std::ostream&)) [with char_t = char; std::ostream = std::basic_ostream]’ 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:130:53: note: no known conversion for argument 1 from ‘void’ to ‘std::ostream& (*)(std::ostream&)’ {aka ‘std::basic_ostream& (*)(std::basic_ostream&)’} 130 | debug_stream_type & operator<<(std::ostream & (*fp)(std::ostream &)) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(int8_t) [with char_t = char; int8_t = signed char]’ 137 | debug_stream_type & operator<<(int8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:137:49: note: no known conversion for argument 1 from ‘void’ to ‘int8_t’ {aka ‘signed char’} 137 | debug_stream_type & operator<<(int8_t const v) | ~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(uint8_t) [with char_t = char; uint8_t = unsigned char]’ 146 | debug_stream_type & operator<<(uint8_t const v) | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:146:50: note: no known conversion for argument 1 from ‘void’ to ‘uint8_t’ {aka ‘unsigned char’} 146 | debug_stream_type & operator<<(uint8_t const v) | ~~~~~~~~~~~~~~^ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/core/debug_stream/debug_stream_type.hpp:189:25: note: candidate: ‘seqan3::debug_stream_type& seqan3::debug_stream_type::operator<<(seqan3::debug_stream_type::fmtflags) [with char_t = char; seqan3::debug_stream_type::fmtflags = std::ios_base::fmtflags]’ ```
Error 9: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 80%] Building CXX object CMakeFiles/structure_file_input_data_out_snippet.dir/io/structure_file/structure_file_input_data_out.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:14: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_output_test.cpp:139:101: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ ```
Error 10: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 81%] Building CXX object CMakeFiles/solution4_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/02_argument_parser/solution4.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector >, seqan3::sam_flag, std::tuple, std::optional, int>, seqan3::sam_tag_dictionary, seqan3::sam_file_header, std::allocator >, std::allocator, std::allocator > > > >*>, seqan3::fields, seqan3::fields, 0>’: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:384:11: required from ‘class seqan3::sam_file_input >, std::vector > >, seqan3::fields, seqan3::type_list >’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:369:78: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp:92:47: error: static assertion failed: You selected a field that was not in field_types_as_ids. ```
Error 11: error: no matching function for call to ‘seqan3::sam_file_output<seqan3::fields<seqan3::field::seq, seqan3::fi ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_move_snippet.dir/io/structure_file/structure_file_input_move.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_sam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_sam]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:590:1: required from here /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:622:46: error: no matching function for call to ‘seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>::emplace_back(__gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type&, __gnu_cxx::__alloc_traits, int>::value_type&, int, __gnu_cxx::__alloc_traits, int>::value_type&, __gnu_cxx::__alloc_traits >, std::vector > > >, std::pair >, std::vector > > >::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, unsigned char>::value_type&, __gnu_cxx::__alloc_traits >, std::vector >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_flag>::value_type&, __gnu_cxx::__alloc_traits, std::optional, int> >, std::tuple, std::optional, int> >::value_type&, __gnu_cxx::__alloc_traits, seqan3::sam_tag_dictionary>::value_type&, seqan3::sam_file_header > >*)’ 622 | ASSERT_NO_THROW(fout.emplace_back(this->seqs[i], | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 623 | this->ids[i], | ~~~~~~~~~~~~~ 624 | this->offsets[i], | ~~~~~~~~~~~~~~~~~ 625 | 0 /*ref_id*/, | ~~~~~~~~~~~~~ 626 | this->ref_offsets[i], | ~~~~~~~~~~~~~~~~~~~~~ 627 | this->alignments[i], | ~~~~~~~~~~~~~~~~~~~~ 628 | cigar_v[i], | ~~~~~~~~~~~ 629 | this->mapqs[i], | ~~~~~~~~~~~~~~~ 630 | this->quals[i], | ~~~~~~~~~~~~~~~ 631 | this->flags[i], | ~~~~~~~~~~~~~~~ 632 | this->mates[i], | ~~~~~~~~~~~~~~~ 633 | this->tag_dicts[i], | ~~~~~~~~~~~~~~~~~~~ ```
Error 12: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_record_iter_snippet.dir/io/structure_file/structure_file_input_record_iter.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp: In member function ‘virtual void bam_format_too_long_cigar_string_read_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:61: error: invalid use of void expression 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:563:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 563 | EXPECT_RANGE_EQ(std::get<0>((*fin.begin()).alignment()), std::get<0>(this->alignments[0])); | ^~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:61: error: invalid use of void expression 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:564:9: note: in expansion of macro ‘EXPECT_RANGE_EQ’ 564 | EXPECT_RANGE_EQ(std::get<1>((*fin.begin()).alignment()), std::get<1>(this->alignments[0])); | ^~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:571:108: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
Error 13: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as s ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_ref_return_snippet.dir/io/structure_file/structure_file_input_ref_return.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp: In instantiation of ‘class seqan3::sam_file_output, seqan3::type_list, seqan3::ref_info_not_given>’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:428:33: required from ‘void gtest_suite_sam_file_write_::write_empty_members::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp:425:1: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:101:19: error: static assertion failed: The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) at the front and not needed otherwise. 101 | static_assert(!selected_field_ids::contains(field::offset), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:105:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_output. Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string from an alignment. 105 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/output.hpp:117:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of seqan3::sam_file_output::field_ids for the accepted values. 111 | []() constexpr | ~~~~~~~~~~~~~~ 112 | { | ~ 113 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 | return false; | ~~~~~~~~~~~~~ 116 | return true; | ~~~~~~~~~~~~ 117 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:62, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/format_bam_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_format_test_template.hpp: In instantiation of ‘void gtest_suite_sam_file_write_::cigar_vector::TestBody() [with gtest_TypeParam_ = seqan3::format_bam]’: ```
Error 14: error: no matching function for call to ‘get<0> ```text [ 63%] Building CXX object io/sam_file/CMakeFiles/sam_file_record_test.dir/sam_file_record_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:26: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp: In function ‘std::vector seqan3::test::operator""_cigar(const char*, std::size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:75: error: no matching function for call to ‘get<0>(std::vector)’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ^ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/10/utility:223:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_OIter1, _OIter2> >::type& std::get(std::pair<_OIter1, _OIter2>&)’ 223 | get(std::pair<_Tp1, _Tp2>& __in) noexcept | ^~~ /usr/include/c++/10/utility:223:5: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:26: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:75: note: ‘std::vector’ is not derived from ‘std::pair<_OIter1, _OIter2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ^ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /usr/include/c++/10/utility:228:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_OIter1, _OIter2> >::type&& std::get(std::pair<_OIter1, _OIter2>&&)’ 228 | get(std::pair<_Tp1, _Tp2>&& __in) noexcept ```
Error 15: error: invalid use of void expression ```text [ 81%] Building CXX object CMakeFiles/dynamic_bitset_set_all_snippet.dir/utility/container/dynamic_bitset_set_all.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:387, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_get_by_member_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:185:26: error: invalid use of void expression 185 | EXPECT_EQ(r.alignment(), alignment_t{}); | ~~~~~~~~~~~^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp: In member function ‘virtual void sam_record_member_types_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:83: error: use of deleted function ‘void std::as_const(const _Tp&&) [with _Tp = int]’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:26:35: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC_’ 26 | #define EXPECT_SAME_TYPE_ESC(...) EXPECT_SAME_TYPE_ESC_(__VA_ARGS__) | ^~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:24:37: note: in expansion of macro ‘EXPECT_SAME_TYPE_ESC’ 24 | #define EXPECT_SAME_TYPE_DEPAREN(X) EXPECT_SAME_TYPE_ESC(EXPECT_SAME_TYPE_ISH X) | ^~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/expect_same_type.hpp:33:45: note: in expansion of macro ‘EXPECT_SAME_TYPE_DEPAREN’ 33 | (std::type_identity{})); | ^~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:221:5: note: in expansion of macro ‘EXPECT_SAME_TYPE’ 221 | EXPECT_SAME_TYPE(int32_t const &, decltype(std::as_const(r.sequence_position()))); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_record_test.cpp:8: ```
Error 16: error: no matching function for call to ‘get<0> ```text [ 81%] Building CXX object CMakeFiles/structure_file_input_skip_fields_snippet.dir/io/structure_file/structure_file_input_skip_fields.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/fixture/io/sam_file/simple_three_verbose_reads_fixture.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp: In function ‘std::vector seqan3::test::operator""_cigar(const char*, std::size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:75: error: no matching function for call to ‘get<0>(std::vector)’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ^ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: /usr/include/c++/10/utility:223:5: note: candidate: ‘template constexpr typename std::tuple_element<_Int, std::pair<_OIter1, _OIter2> >::type& std::get(std::pair<_OIter1, _OIter2>&)’ 223 | get(std::pair<_Tp1, _Tp2>& __in) noexcept | ^~~ /usr/include/c++/10/utility:223:5: note: template argument deduction/substitution failed: In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/fixture/io/sam_file/simple_three_verbose_reads_fixture.hpp:20, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/literal/cigar_literal.hpp:24:75: note: ‘std::vector’ is not derived from ‘std::pair<_OIter1, _OIter2>’ 24 | return std::get<0>(seqan3::detail::parse_cigar(std::string_view{s, n})); | ^ In file included from /usr/include/c++/10/optional:36, from /usr/include/c++/10/ranges:45, from /usr/include/c++/10/bits/ranges_algobase.h:38, from /usr/include/c++/10/bits/ranges_uninitialized.h:36, from /usr/include/c++/10/memory:69, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:57, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_seek_test.cpp:8: ```
Error 17: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sa ```text [ 83%] Building CXX object CMakeFiles/structure_file_output_write_std_out_snippet.dir/io/structure_file/structure_file_output_write_std_out.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp: In instantiation of ‘class seqan3::sam_file_input >, const std::vector > >, seqan3::fields, seqan3::type_list >’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:539:114: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:363:19: error: static assertion failed: The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an alignment from the cigar information. 363 | static_assert(!selected_field_ids::contains(field::alignment), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:379:10: error: static assertion failed: You selected a field that is not valid for SAM files, please refer to the documentation of sam_file_input::field_ids for the accepted values. 373 | []() constexpr | ~~~~~~~~~~~~~~ 374 | { | ~ 375 | for (field f : selected_field_ids::as_array) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 376 | if (!field_ids::contains(f)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 377 | return false; | ~~~~~~~~~~~~~ 378 | return true; | ~~~~~~~~~~~~ 379 | }(), | ~^~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/sam_file/input.hpp:33, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/io/sam_file/sam_file_input_test.cpp:17: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/io/detail/record.hpp: In instantiation of ‘struct seqan3::detail::select_types_with_ids >, std::__cxx11::basic_string, std::allocator >, std::optional, std::optional, std::vector >, unsigned char, std::vector
github-actions[bot] commented 1 year ago

Failure on gcc11

See https://github.com/seqan/seqan3/actions/runs/4969996412 for more information.

Error 1: error: ‘seqan’ was not declared in this scope ```text [ 54%] Building CXX object core/algorithm/detail/CMakeFiles/execution_handler_sequential_test.dir/execution_handler_sequential_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_sequential_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_sequential_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: ‘sequence’ was not declared in this scope ```
Error 2: error: ‘seqan’ was not declared in this scope ```text [ 54%] Building CXX object core/algorithm/detail/CMakeFiles/execution_handler_parallel_test.dir/execution_handler_parallel_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_parallel_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_parallel_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: ‘sequence’ was not declared in this scope ```
Error 3: error: ‘seqan’ was not declared in this scope ```text [ 72%] Building CXX object search/CMakeFiles/search_scheme_algorithm_test.dir/search_scheme_algorithm_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/search/search_scheme_algorithm_test.cpp:23: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/search/search_scheme_algorithm_test.cpp:23: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: expected ‘auto’ or ‘decltype(auto)’ after ‘sequence’ 151 | seqan::String sequence; | ^~~~~~~~ ```
Error 4: error: ‘seqan’ was not declared in this scope ```text [ 82%] Building CXX object test/CMakeFiles/expect_range_eq_test.dir/expect_range_eq_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:13: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:24:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 24 | using seqan2_container_types = ::testing::Types, seqan::StringSet>; | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:24:89: error: template argument 1 is invalid 24 | using seqan2_container_types = ::testing::Types, seqan::StringSet>; | ^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:24:43: error: ‘’ in namespace ‘testing’ does not name a type 24 | using seqan2_container_types = ::testing::Types, seqan::StringSet>; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:71, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:25:36: error: ‘seqan2_container_types’ was not declared in this scope; did you mean ‘seqan2_container’? 25 | TYPED_TEST_SUITE(seqan2_container, seqan2_container_types, ); | ^~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:25:1: error: template argument 1 is invalid 25 | TYPED_TEST_SUITE(seqan2_container, seqan2_container_types, ); | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:25:1: error: expected initializer before ‘gtest_type_params_seqan2_container_’ 25 | TYPED_TEST_SUITE(seqan2_container, seqan2_container_types, ); | ^~~~~~~~~~~~~~~~ ```
Error 5: error: ‘seqan’ was not declared in this scope ```text [ 82%] Building CXX object test/CMakeFiles/tmp_directory_test.dir/tmp_directory_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/sequence_generator_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/sequence_generator_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: ‘sequence’ was not declared in this scope 151 | seqan::String sequence; | ^~~~~~~~ ```
Error 6: error: ‘seqan’ was not declared in this scope ```text [ 90%] Building CXX object utility/simd/views/CMakeFiles/to_simd_test.dir/to_simd_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/utility/simd/views/to_simd_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/utility/simd/views/to_simd_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: ‘sequence’ was not declared in this scope 151 | seqan::String sequence; | ^~~~~~~~ ```
github-actions[bot] commented 1 year ago

Failure on gcc12

See https://github.com/seqan/seqan3/actions/runs/4969996412 for more information.

Error 1: error: ‘seqan’ was not declared in this scope ```text [ 70%] Building CXX object CMakeFiles/search_basic_index_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/09_search/search_basic_index.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_sequential_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: ‘sequence’ was not declared in this scope 151 | seqan::String sequence; | ^~~~~~~~ ```
Error 2: error: ‘seqan’ was not declared in this scope ```text [ 54%] Building CXX object core/algorithm/detail/CMakeFiles/execution_handler_parallel_test.dir/execution_handler_parallel_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_template.hpp:18, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/core/algorithm/detail/execution_handler_parallel_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: ‘sequence’ was not declared in this scope 151 | seqan::String sequence; | ^~~~~~~~ ```
Error 3: error: ‘seqan’ was not declared in this scope ```text [ 85%] Linking CXX executable std/view/subrange_snippet In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/search/search_scheme_algorithm_test.cpp:23: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ ```
Error 4: error: ‘seqan’ has not been declared ```text [ 85%] Building CXX object CMakeFiles/seed_example_snippet.dir/home/runner/work/seqan3/seqan3/seqan3-build/api_stability_snippet-prefix/src/api_stability_snippet/doc/tutorial/06_minimisers/seed_example.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: expected ‘auto’ or ‘decltype(auto)’ after ‘sequence’ 151 | seqan::String sequence; | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:39: error: missing template arguments before ‘;’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:155:21: error: expected ‘auto’ or ‘decltype(auto)’ after ‘sequence’ 155 | appendValue(sequence, static_cast(dis_alpha(gen))); | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:155:29: error: missing template arguments before ‘,’ token 155 | appendValue(sequence, static_cast(dis_alpha(gen))); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:157:12: error: expected ‘auto’ or ‘decltype(auto)’ after ‘sequence’ ```
Error 5: error: ‘seqan’ was not declared in this scope ```text [ 82%] Building CXX object test/CMakeFiles/expect_range_eq_test.dir/expect_range_eq_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:13: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:24:49: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 24 | using seqan2_container_types = ::testing::Types, seqan::StringSet>; | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:24:89: error: template argument 1 is invalid 24 | using seqan2_container_types = ::testing::Types, seqan::StringSet>; | ^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:24:43: error: ‘’ in namespace ‘testing’ does not name a type 24 | using seqan2_container_types = ::testing::Types, seqan::StringSet>; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit-build/_deps/gtest_fetch_content-src/googletest/include/gtest/gtest.h:71, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:8: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:25:36: error: ‘seqan2_container_types’ was not declared in this scope; did you mean ‘seqan2_container’? 25 | TYPED_TEST_SUITE(seqan2_container, seqan2_container_types, ); | ^~~~~~~~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:25:1: error: template argument 1 is invalid 25 | TYPED_TEST_SUITE(seqan2_container, seqan2_container_types, ); | ^~~~~~~~~~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/seqan2_test.cpp:25:1: error: expected initializer before ‘gtest_type_params_seqan2_container_’ 25 | TYPED_TEST_SUITE(seqan2_container, seqan2_container_types, ); | ^~~~~~~~~~~~~~~~ ```
Error 6: error: ‘seqan’ was not declared in this scope ```text [ 82%] Building CXX object test/CMakeFiles/tmp_directory_test.dir/tmp_directory_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/test/sequence_generator_test.cpp:12: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: ‘sequence’ was not declared in this scope 151 | seqan::String sequence; | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_pairs_seqan2(size_t, size_t, size_t)’: ```
Error 7: error: ‘seqan’ was not declared in this scope ```text [ 90%] Building CXX object utility/simd/views/CMakeFiles/to_simd_test.dir/to_simd_test.cpp.o In file included from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:21, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/utility/simd/views/to_simd_test.cpp:19: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:35: error: ‘seqan’ was not declared in this scope; did you mean ‘seqan3’? 47 | struct indirectly_readable_traits> | ^~~~~ | seqan3 /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/seqan2.hpp:47:56: error: template argument 1 is invalid 47 | struct indirectly_readable_traits> | ^~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_seqan2(size_t, size_t, size_t)’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:56: error: ‘seqan’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:83: error: expected primary-expression before ‘>’ token 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:148:86: error: ‘::VALUE’ has not been declared 148 | std::uniform_int_distribution dis_alpha(0, seqan::ValueSize::VALUE - 1); | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:5: error: ‘seqan’ has not been declared 151 | seqan::String sequence; | ^~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:29: error: expected primary-expression before ‘>’ token 151 | seqan::String sequence; | ^ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp:151:31: error: ‘sequence’ was not declared in this scope 151 | seqan::String sequence; | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/include/seqan3/test/performance/sequence_generator.hpp: In function ‘auto seqan3::test::generate_sequence_pairs_seqan2(size_t, size_t, size_t)’: ```
github-actions[bot] commented 1 year ago

Failure on gcc13

See https://github.com/seqan/seqan3/actions/runs/5035288062 for more information.

Error 1: error: no match for call to ‘ ```text [ 96%] Building CXX object utility/views/CMakeFiles/type_reduce_test.dir/type_reduce_test.cpp.o /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/utility/views/zip_test.cpp: In member function ‘virtual void zip_test_basic_Test::TestBody()’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/utility/views/zip_test.cpp:147:51: error: no match for call to ‘(const seqan::std::ranges::zip_fn) (zip_test::other_range_t&)’ 147 | auto zip_view = range | seqan3::views::zip(other_range); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/utility/views/zip.hpp:15, from /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/utility/views/zip_test.cpp:15: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:547:20: note: candidate: ‘template requires ((... && viewable_range)) && sizeof ... (urng_ts ...) == 0 constexpr auto seqan::std::ranges::zip_fn::operator()(urng_ts&& ...) const’ 547 | constexpr auto operator()(urng_ts &&... ranges) const | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:547:20: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:547:20: note: constraints not satisfied /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp: In substitution of ‘template requires ((... && viewable_range)) && sizeof ... (urng_ts ...) == 0 constexpr auto seqan::std::ranges::zip_fn::operator()(urng_ts&& ...) const [with urng_ts = {std::vector, std::allocator >, std::allocator, std::allocator > > >&}]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/utility/views/zip_test.cpp:147:51: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:547:20: required by the constraints of ‘template requires ((... && viewable_range)) && sizeof ... (urng_ts ...) == 0 constexpr auto seqan::std::ranges::zip_fn::operator()(urng_ts&& ...) const’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:546:38: note: the expression ‘sizeof ... (urng_ts ...) == 0 [with urng_ts = {std::vector, std::allocator >, std::allocator, std::allocator > > >&}]’ evaluated to ‘false’ 546 | requires (sizeof...(urng_ts) == 0) | ~~~~~~~~~~~~~~~~~~~~^~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:554:20: note: candidate: ‘template requires ((... && viewable_range)) && sizeof ... (urng_ts ...) > 1 constexpr auto seqan::std::ranges::zip_fn::operator()(urng_ts&& ...) const’ 554 | constexpr auto operator()(urng_ts &&... ranges) const | ^~~~~~~~ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:554:20: note: template argument deduction/substitution failed: /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:554:20: note: constraints not satisfied /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp: In substitution of ‘template requires ((... && viewable_range)) && sizeof ... (urng_ts ...) > 1 constexpr auto seqan::std::ranges::zip_fn::operator()(urng_ts&& ...) const [with urng_ts = {std::vector, std::allocator >, std::allocator, std::allocator > > >&}]’: /home/runner/work/seqan3/seqan3/seqan3-build/api_stability_unit-prefix/src/api_stability_unit/test/unit/utility/views/zip_test.cpp:147:51: required from here /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:554:20: required by the constraints of ‘template requires ((... && viewable_range)) && sizeof ... (urng_ts ...) > 1 constexpr auto seqan::std::ranges::zip_fn::operator()(urng_ts&& ...) const’ /home/runner/work/seqan3/seqan3/seqan3/include/seqan3/contrib/std/zip_view.hpp:553:38: note: the expression ‘sizeof ... (urng_ts ...) > 1 [with urng_ts = {std::vector, std::allocator >, std::allocator, std::allocator > > >&}]’ evaluated to ‘false’ 553 | requires (sizeof...(urng_ts) > 1) | ~~~~~~~~~~~~~~~~~~~~^~~~ gmake[5]: *** [utility/views/CMakeFiles/zip_test.dir/build.make:66: utility/views/CMakeFiles/zip_test.dir/zip_test.cpp.o] Error 1 ```
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