cobs: add aarch64/arm64 builds

martin-g commented 1 day ago

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martin-g commented 1 day ago

Some tests fail on OSX ARM64:

11:43:40 [32mBIOCONDA INFO[0m (OUT) x subsampled_integration_test/COBS_out/neisseria_gonorrhoeae__01.cobs_classic[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [ RUN      ] mof_integration.queries__mof_tests[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) DIE: Assertion "page_size == 4096" failed! @ $SRC_DIR/cobs/util/misc.cpp:43[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) libc++abi: terminating[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)       Start 37: non_acgt_test.non_acgt_test_main_test[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) 37/44 Test #37: non_acgt_test.non_acgt_test_main_test ...................................Subprocess aborted***Exception:   0.01 sec[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) Running main() from $SRC_DIR/extlib/googletest/googletest/src/gtest_main.cc[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) Note: Google Test filter = non_acgt_test.non_acgt_test_main_test[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [==========] Running 1 test from 1 test suite.[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [----------] Global test environment set-up.[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [----------] 1 test from non_acgt_test[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [ RUN      ] non_acgt_test.non_acgt_test_main_test[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) DIE: Assertion "page_size == 4096" failed! @ $SRC_DIR/cobs/util/misc.cpp:43[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) libc++abi: terminating[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)       Start 38: parameters.false_positive[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) 38/44 Test #38: parameters.false_positive ...............................................   Passed    0.02 sec[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)       Start 39: parameters.false_positive_hash[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) 39/44 Test #39: parameters.false_positive_hash ..........................................   Passed    0.02 sec[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)       Start 40: parameters.canonical[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) 40/44 Test #40: parameters.canonical ....................................................   Passed    0.01 sec[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)       Start 41: text.process_txt1[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) 41/44 Test #41: text.process_txt1 .......................................................   Passed    0.01 sec[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)       Start 42: text.document_list[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) 42/44 Test #42: text.document_list ......................................................   Passed    0.00 sec[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)       Start 43: util.allocate_aligned[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) 43/44 Test #43: util.allocate_aligned ...................................................Subprocess aborted***Exception:   0.00 sec[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) Running main() from $SRC_DIR/extlib/googletest/googletest/src/gtest_main.cc[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) Note: Google Test filter = util.allocate_aligned[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [==========] Running 1 test from 1 test suite.[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [----------] Global test environment set-up.[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [----------] 1 test from util[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [ RUN      ] util.allocate_aligned[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) DIE: Assertion "page_size == 4096" failed! @ $SRC_DIR/cobs/util/misc.cpp:43[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) libc++abi: terminating[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)       Start 44: util.kmer_canonicalize[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) 44/44 Test #44: util.kmer_canonicalize ..................................................   Passed    0.00 sec[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) 64% tests passed, 16 tests failed out of 44[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) Total Test time (real) =   6.87 sec[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) [0m
11:43:40 [32mBIOCONDA INFO[0m (OUT) The following tests FAILED:[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)     2 - classic_index_construction.combine (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)     5 - classic_index_query.all_included_small_batch (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)     6 - classic_index_query.one_included_small_batch (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)     7 - classic_index_query.one_included_large_batch (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)     8 - classic_index_query.false_positive (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)     9 - classic_index_query.one_included_large_batch_multi_index (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    12 - compact_index_query.all_included_mmap_small (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    13 - compact_index_query.all_included_mmap (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    14 - compact_index_query.one_included_mmap (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    15 - compact_index_query.false_positive_mmap (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    22 - fasta.document_list (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    26 - fasta_multi.document_list (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    28 - fastq.document_list (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    36 - mof_integration.queries__mof_tests (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    37 - non_acgt_test.non_acgt_test_main_test (Subprocess aborted)[0m
11:43:40 [32mBIOCONDA INFO[0m (OUT)    43 - util.allocate_aligned (Subprocess aborted)[0m

martin-g commented 1 day ago

@BiocondaBot please fetch artifacts

BiocondaBot commented 1 day ago

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	cobs-0.3.1-hdcf5f25_1.tar.bz2	linux-64.zip	GitHub Actions	show You may also use `conda` to install after downloading and extracting the zip file. `conda install -c ./packages <package name>`
osx-64	cobs-0.3.1-h63051a7_1.tar.bz2	osx-64.zip	GitHub Actions	show You may also use `conda` to install after downloading and extracting the zip file. `conda install -c ./packages <package name>`
linux-aarch64	cobs-0.3.1-h7f4e536_1.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/ec25e75f-6d92-4ff3-9aff-95ef3f7ae690/artifacts/0/tmp/artifacts/packages <package name>`

Docker image(s) built:

Package	Tag	CI	Install with `docker`
cobs	0.3.1--hdcf5f25_1	GitHub Actions	show Images are in the linux-64 zip file above.`gzip -dc images/cobs---0.3.1--hdcf5f25_1.tar.gz \\| docker load`

martin-g commented 1 day ago

mgrigorov in 🌐 euler-arm-22 in /tmp via 🅒 test123 
❯ tar xvf cobs-0.3.1-h7f4e536_1.tar.bz2                                                                                                                                                                    (test123) 
info/test/run_test.sh
info/run_exports.json
info/hash_input.json
info/index.json
info/recipe/build.sh
info/recipe/meta.yaml.template
info/licenses/LICENSE
info/has_prefix
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/files
info/about.json
info/paths.json
info/git
info/recipe/cobs-aarch64.patch
include/gmock/internal/custom/gmock-generated-actions.h
include/gtest/internal/custom/gtest.h
include/gtest/internal/custom/gtest-port.h
include/gmock/internal/custom/gmock-matchers.h
include/gmock/internal/custom/gmock-port.h
include/gtest/internal/custom/gtest-printers.h
include/gtest/gtest_prod.h
include/gmock/gmock-more-matchers.h
include/gmock/gmock.h
include/gtest/internal/gtest-port-arch.h
include/gmock/internal/gmock-port.h
include/gmock/gmock-cardinalities.h
include/gtest/internal/gtest-type-util.h
include/gtest/gtest-test-part.h
include/gtest/internal/gtest-string.h
include/gtest/gtest-message.h
include/gtest/gtest-assertion-result.h
include/gtest/internal/gtest-filepath.h
include/gmock/gmock-nice-strict.h
include/gtest/gtest_pred_impl.h
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include/xxhash.h
include/gmock/internal/gmock-pp.h
include/gtest/internal/gtest-death-test-internal.h
include/gtest/gtest-death-test.h
include/gtest/gtest-typed-test.h
include/gmock/internal/gmock-internal-utils.h
include/gtest/gtest-param-test.h
include/gmock/gmock-function-mocker.h
include/gtest/gtest-matchers.h
include/gtest/internal/gtest-param-util.h
include/gtest/gtest-printers.h
include/gmock/gmock-more-actions.h
include/gtest/internal/gtest-internal.h
include/gmock/gmock-spec-builders.h
include/gmock/gmock-actions.h
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include/tlx/simple_vector.hpp
include/tlx/timestamp.hpp
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include/tlx/unused.hpp
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include/tlx/string/parse_si_iec_units.hpp
include/tlx/sort/networks/cswap.hpp
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include/tlx/string/expand_environment_variables.hpp
include/tlx/algorithm/is_sorted_cmp.hpp
include/tlx/meta/apply_tuple.hpp
include/tlx/algorithm/exclusive_scan.hpp
include/tlx/logger/unordered_set.hpp
include/tlx/meta/log2.hpp
include/tlx/logger/map.hpp
include/tlx/meta/call_foreach.hpp
include/tlx/string/contains_word.hpp
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include/tlx/string/join.hpp
include/tlx/string/less_icase.hpp
include/tlx/meta.hpp
include/tlx/math/is_power_of_two.hpp
include/tlx/meta/fold_left_tuple.hpp
include/tlx/meta/vmap_foreach_tuple.hpp
include/tlx/meta/fold_right_tuple.hpp
include/tlx/meta/call_foreach_tuple_with_index.hpp
include/tlx/logger/unordered_map.hpp
include/tlx/math/bswap_be.hpp
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include/tlx/meta/vmap_foreach.hpp
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include/tlx/meta/fold_right.hpp
include/tlx/string/parse_uri.hpp
include/tlx/meta/call_foreach_with_index.hpp
include/tlx/meta/call_for_range.hpp
include/tlx/string/hash_sdbm.hpp
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include/tlx/meta/vmap_foreach_with_index.hpp
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include/tlx/digest/md5.hpp
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include/tlx/string/ends_with.hpp
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include/tlx/meta/vmap_for_range.hpp
include/tlx/string/ssprintf_generic.hpp
include/tlx/digest/sha256.hpp
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include/tlx/allocator_base.hpp
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include/tlx/thread_barrier_spin.hpp
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include/tlx/thread_pool.hpp
include/tlx/meta/has_method.hpp
include/tlx/sort/strings/multikey_quicksort.hpp
include/tlx/stack_allocator.hpp
include/tlx/algorithm/merge_advance.hpp
include/tlx/string/levenshtein.hpp
include/tlx/meta/function_chain.hpp
include/tlx/meta/function_stack.hpp
include/tlx/math/aggregate.hpp
include/tlx/math/polynomial_regression.hpp
include/tlx/string/trim.hpp
include/tlx/logger/core.hpp
include/tlx/sort/strings/insertion_sort.hpp
include/tlx/container/simple_vector.hpp
include/tlx/container/d_ary_heap.hpp
include/tlx/siphash.hpp
include/tlx/string/split.hpp
include/tlx/container/lru_cache.hpp
include/tlx/algorithm/multiway_merge_splitting.hpp
include/tlx/algorithm/multisequence_selection.hpp
include/tlx/algorithm/multisequence_partition.hpp
include/tlx/sort/strings_parallel.hpp
include/tlx/container/splay_tree.hpp
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include/tlx/sort/networks/bose_nelson.hpp
include/tlx/container/d_ary_addressable_int_heap.hpp
include/tlx/die/core.hpp
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include/tlx/counting_ptr.hpp
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include/tlx/sort/strings/sample_sort_tools.hpp
include/tlx/container/loser_tree.hpp
include/tlx/sort/strings/radix_sort.hpp
include/tlx/algorithm/multiway_merge.hpp
include/tlx/sort/strings/parallel_sample_sort.hpp
include/tlx/container/btree.hpp
include/gmock/internal/custom/README.md
include/gtest/internal/custom/README.md
share/man/man1/xxhsum.1
lib/libgtest_main.a
lib/libgmock_main.a
lib/libxxhash.a
lib/libgmock.a
lib/libgtest.a
lib/libtlx.a
lib/cmake/tlx/tlx-version.cmake
lib/cmake/tlx/tlx-targets-release.cmake
lib/cmake/GTest/GTestConfig.cmake
lib/cmake/tlx/tlx-config.cmake
lib/cmake/GTest/GTestConfigVersion.cmake
lib/cmake/GTest/GTestTargets-release.cmake
lib/cmake/tlx/tlx-targets.cmake
lib/cmake/GTest/GTestTargets.cmake
bin/xxhsum
bin/cobs
lib/pkgconfig/tlx.pc
lib/pkgconfig/gtest.pc
lib/pkgconfig/gmock.pc
lib/pkgconfig/gtest_main.pc
lib/pkgconfig/gmock_main.pc

mgrigorov in 🌐 euler-arm-22 in /tmp via 🅒 test123 
❯ ./bin/cobs  
(Co)mpact (B)it-Sliced (S)ignature Index for Genome Search (version 0.3.1)

Usage: /tmp/cccc/bin/cobs <subtool> ...

Available subtools: 
  doc-list                   read a list of documents and print the list
  doc-dump                   read a list of documents and dump their contents
  classic-construct          constructs a classic index from the documents in <in_dir>
  classic-construct-random   constructs a classic index with random content
  compact-construct          creates the folders used for further construction
  compact-construct-combine  combines the classic indices in <in_dir> to form a compact index
  classic-combine            combines the classic indices in <in_dir>
  query                      query an index
  print-parameters           calculates index parameters
  print-kmers                print all canonical kmers from <query>
  benchmark-fpr              run benchmark and false positive measurement
  generate-queries           select queries randomly from documents
  version                    prints version and exit

See https://panthema.net/cobs for more information on COBS.

LGTM!

martin-g commented 1 day ago

@BiocondaBot please add label

bioconda / bioconda-recipes