Closed hchetia closed 3 years ago
I tried a similar approach in MacOS with g++ version MacPorts gcc10 10.2.0_1 and got a different error.
In file included from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.cpp:23: /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.hh: In member function 'ehunter::NumericInterval ehunter::RepeatGenotype::shortAlleleSizeInUnitsCi() const': /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.hh:65:80: error: implicitly-declared 'constexpr ehunter::NumericInterval::NumericInterval(const ehunter::NumericInterval&)' is deprecated [-Werror=deprecated-copy] 65 | NumericInterval shortAlleleSizeInUnitsCi() const { return alleles_.front().ci; } | ^~ In file included from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.hh:32, from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.cpp:23: /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/common/Common.hh:82:22: note: because 'ehunter::NumericInterval' has user-provided 'ehunter::NumericInterval& ehunter::NumericInterval::operator=(const ehunter::NumericInterval&)' 82 | NumericInterval& operator=(const NumericInterval& other) | ^~~~~~~~ In file included from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.cpp:23: /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.hh: In member function 'ehunter::NumericInterval ehunter::RepeatGenotype::longAlleleSizeInUnitsCi() const': /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.hh:84:78: error: implicitly-declared 'constexpr ehunter::NumericInterval::NumericInterval(const ehunter::NumericInterval&)' is deprecated [-Werror=deprecated-copy] 84 | NumericInterval longAlleleSizeInUnitsCi() const { return alleles_.back().ci; } | ^~ In file included from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.hh:32, from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.cpp:23: /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/common/Common.hh:82:22: note: because 'ehunter::NumericInterval' has user-provided 'ehunter::NumericInterval& ehunter::NumericInterval::operator=(const ehunter::NumericInterval&)' 82 | NumericInterval& operator=(const NumericInterval& other) | ^~~~~~~~ /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.cpp: In function 'std::ostream& ehunter::operator<<(std::ostream&, const ehunter::RepeatGenotype&)': /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.cpp:65:12: error: implicitly-declared 'constexpr ehunter::NumericInterval::NumericInterval(const ehunter::NumericInterval&)' is deprecated [-Werror=deprecated-copy] 65 | out << shortAlleleCi; | ^~~~~~~~~~~~~ In file included from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.hh:32, from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.cpp:23: /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/common/Common.hh:82:22: note: because 'ehunter::NumericInterval' has user-provided 'ehunter::NumericInterval& ehunter::NumericInterval::operator=(const ehunter::NumericInterval&)' 82 | NumericInterval& operator=(const NumericInterval& other) | ^~~~~~~~ /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/common/Common.hh:123:61: note: initializing argument 2 of 'std::ostream& ehunter::operator<<(std::ostream&, ehunter::NumericInterval)' 123 | std::ostream& operator<<(std::ostream& out, NumericInterval numericInterval); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.cpp:71:23: error: implicitly-declared 'constexpr ehunter::NumericInterval::NumericInterval(const ehunter::NumericInterval&)' is deprecated [-Werror=deprecated-copy] 71 | out << "/" << longAlleleCi; | ^~~~~~~~~~~~ In file included from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.hh:32, from /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/genotyping/RepeatGenotype.cpp:23: /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/common/Common.hh:82:22: note: because 'ehunter::NumericInterval' has user-provided 'ehunter::NumericInterval& ehunter::NumericInterval::operator=(const ehunter::NumericInterval&)' 82 | NumericInterval& operator=(const NumericInterval& other) | ^~~~~~~~ /Users/hasnahana/Downloads/ExpansionHunter-4.0.2_2/common/Common.hh:123:61: note: initializing argument 2 of 'std::ostream& ehunter::operator<<(std::ostream&, ehunter::NumericInterval)' 123 | std::ostream& operator<<(std::ostream& out, NumericInterval numericInterval); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ cc1plus: all warnings being treated as errors make[2]: *** [genotyping/CMakeFiles/genotyping.dir/RepeatGenotype.cpp.o] Error 1 make[1]: *** [genotyping/CMakeFiles/genotyping.dir/all] Error 2 make: *** [all] Error 2
Hi Hasna,
Apologies for the slow reply. We are about to release a new version of ExpansionHunter that will include an updated build script. Could you please try building the new version when it is released?
Best wishes, Egor
@hchetia, the new version was just released. Could you please check if you can build the new version?
Hi Egor,
Thanks for the new release. Let me try building and get back to you! Best, Hasna
Hi Egor, I tried building the EH 5.0. Cmake step went fine but make failed with two errors shown below-
In file included from /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndex.cpp:31: /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:946:33: error: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>, spp::sparsegroup<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>, spp::libc_allocator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>>> *, std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>> *, std::__1::input_iterator_tag, spp::libc_allocator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>>>' is deprecated because it has a user-declared copy assignment operator [-Werror,-Wdeprecated-copy] Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>, spp::sparsegroup<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>, spp::libc_allocator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>>> *, std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>> *, std::__1::input_iterator_tag, spp::libc_allocator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>>>' first required here for (destructive_iterator it = ht.destructive_begin(); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>>::SelectKey, spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>>::SetKey, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>>>::_move_from' requested here _move_from(mover, ht, min_buckets_wanted); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>>::SelectKey, spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>>::SetKey, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>>>::sparse_hashtable' requested here sparse_hashtable tmp(MoveDontCopy, *this, resize_to); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>>::SelectKey, spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>>::SetKey, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>>>::_resize_delta' requested here if (_resize_delta(1)) ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:3812:29: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>>::SelectKey, spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>>::SetKey, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>>>::find_or_insert<spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>>::DefaultValue, const unsigned int &>' requested here return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second; ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndex.cpp:132:34: note: in instantiation of function template specialization 'spp::sparse_hash_map<unsigned int, std::__1::vector<graphtools::Path>, spp::spp_hash<uint32_t>, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, std::__1::vector<graphtools::Path>>>>::operator[]<const unsigned int &>' requested here kmer_to_paths_map[expanded_kmer_key] = { MiniPathToPath(miniPathIter->second), kmer_path }; ^ In file included from /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndex.cpp:31: /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:946:33: error: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::__1::pair<const unsigned int, graphtools::MiniPath>, spp::sparsegroup<std::__1::pair<const unsigned int, graphtools::MiniPath>, spp::libc_allocator<std::__1::pair<const unsigned int, graphtools::MiniPath>>> *, std::__1::pair<const unsigned int, graphtools::MiniPath> *, std::__1::input_iterator_tag, spp::libc_allocator<std::__1::pair<const unsigned int, graphtools::MiniPath>>>' is deprecated because it has a user-declared copy assignment operator [-Werror,-Wdeprecated-copy] Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::__1::pair<const unsigned int, graphtools::MiniPath>, spp::sparsegroup<std::__1::pair<const unsigned int, graphtools::MiniPath>, spp::libc_allocator<std::__1::pair<const unsigned int, graphtools::MiniPath>>> *, std::__1::pair<const unsigned int, graphtools::MiniPath> *, std::__1::input_iterator_tag, spp::libc_allocator<std::__1::pair<const unsigned int, graphtools::MiniPath>>>' first required here for (destructive_iterator it = ht.destructive_begin(); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable<std::__1::pair<const unsigned int, graphtools::MiniPath>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, graphtools::MiniPath>::SelectKey, spp::sparse_hash_map<unsigned int, graphtools::MiniPath>::SetKey, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, graphtools::MiniPath>>>::_move_from' requested here _move_from(mover, ht, min_buckets_wanted); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable<std::__1::pair<const unsigned int, graphtools::MiniPath>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, graphtools::MiniPath>::SelectKey, spp::sparse_hash_map<unsigned int, graphtools::MiniPath>::SetKey, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, graphtools::MiniPath>>>::sparse_hashtable' requested here sparse_hashtable tmp(MoveDontCopy, *this, resize_to); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:3217:9: note: in instantiation of member function 'spp::sparse_hashtable<std::__1::pair<const unsigned int, graphtools::MiniPath>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, graphtools::MiniPath>::SelectKey, spp::sparse_hash_map<unsigned int, graphtools::MiniPath>::SetKey, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, graphtools::MiniPath>>>::_resize_delta' requested here _resize_delta(1); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/external/sparsepp/sparsepp-e40d7a0/sparsepp/spp.h:3849:20: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::__1::pair<const unsigned int, graphtools::MiniPath>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, graphtools::MiniPath>::SelectKey, spp::sparse_hash_map<unsigned int, graphtools::MiniPath>::SetKey, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, graphtools::MiniPath>>>::emplace<const unsigned int &, graphtools::MiniPath &>' requested here return rep.emplace(std::forward<Args>(args)...); ^ /Users/hasnahana/Downloads/ExpansionHunter-5.0.0/ehunter/thirdparty/graph-tools-master-f421f4c/src/graphalign/KmerIndex.cpp:145:43: note: in instantiation of function template specialization 'spp::sparse_hash_map<unsigned int, graphtools::MiniPath, spp::spp_hash<uint32_t>, std::__1::equal_to<unsigned int>, spp::libc_allocator<std::__1::pair<const unsigned int, graphtools::MiniPath>>>::emplace<const unsigned int &, graphtools::MiniPath &>' requested here kmer_to_minipaths_map.emplace(expanded_kmer_key, miniPath); ^ 2 errors generated. make[5]: *** [thirdparty/graph-tools-master-f421f4c/CMakeFiles/graphtools.dir/src/graphalign/KmerIndex.cpp.o] Error 1 make[4]: *** [thirdparty/graph-tools-master-f421f4c/CMakeFiles/graphtools.dir/all] Error 2 make[3]: *** [all] Error 2 make[2]: *** [ehunter-prefix/src/ehunter-stamp/ehunter-build] Error 2 make[1]: *** [CMakeFiles/ehunter.dir/all] Error 2 make: *** [all] Error 2
Thanks @hchetia,
Can you confirm your OS/compiler version? You had mentioned earlier this was:
GCC version- 9.3.0 In CentOS Linux release 7.9.2009 (Core)
...if this is the case, it is an interesting problem because we've compiled under a very similar configuration, using the devtoolset release of gcc9. Is it possible the cmake configuration is picking up a different gcc version? Can you share your cmake command-line and the cmake output?
Hi @ctsa , yes my GCC version is gcc version 9.3.0 (crosstool-NG 1.24.0.133_b0863d8_dirty) OS is CentOS Linux release 7.9.2009 (Core)
I ran a cmake .. in build dir;
log shown below-
-- The C compiler identification is GNU 9.3.0 -- The CXX compiler identification is GNU 9.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/bin/x86_64-conda-linux-gnu-cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/bin/x86_64-conda-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/libz.so (found version "1.2.11") -- Found BZip2: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for lzma_auto_decoder in /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/liblzma.so -- Looking for lzma_auto_decoder in /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/liblzma.so - found -- Looking for lzma_easy_encoder in /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/liblzma.so -- Looking for lzma_easy_encoder in /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/liblzma.so - found -- Looking for lzma_lzma_preset in /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/liblzma.so -- Looking for lzma_lzma_preset in /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/liblzma.so - found -- Found LibLZMA: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/liblzma.so (found version "5.2.5") -- Found CURL: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/lib/libcurl.so (found version "7.78.0") -- Found Git: /usr/bin/git (found version "1.8.3.1") -- Configuring done -- Generating done -- Build files have been written to: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build
I follow this with make. The make error is shown below-
`[ 2%] Creating directories for 'abseil'
[ 4%] Performing download step (git clone) for 'abseil'
Cloning into 'abseil'...
HEAD is now at 278e0a0... Abseil LTS 20210324, Patch 2
[ 6%] No update step for 'abseil'
[ 8%] No patch step for 'abseil'
[ 10%] Performing configure step for 'abseil'
-- The CXX compiler identification is GNU 9.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/abseil-prefix/src/abseil-build
[ 12%] Performing build step for 'abseil'
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[ 49%] Building CXX object absl/container/CMakeFiles/hashtablez_sampler.dir/internal/hashtablez_sampler.cc.o
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[ 84%] Linking CXX static library libabsl_random_internal_randen_hwaes_impl.a
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[ 85%] Building CXX object absl/random/CMakeFiles/random_internal_randen_hwaes.dir/internal/randen_detect.cc.o
[ 86%] Linking CXX static library libabsl_random_internal_randen_hwaes.a
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[ 90%] Building CXX object absl/random/CMakeFiles/random_internal_randen.dir/internal/randen.cc.o
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[ 91%] Building CXX object absl/random/CMakeFiles/random_internal_pool_urbg.dir/internal/pool_urbg.cc.o
[ 91%] Linking CXX static library libabsl_random_internal_pool_urbg.a
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[ 92%] Building CXX object absl/random/CMakeFiles/random_distributions.dir/discrete_distribution.cc.o
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[ 94%] Building CXX object absl/random/CMakeFiles/random_seed_sequences.dir/seed_sequences.cc.o
[ 94%] Linking CXX static library libabsl_random_seed_sequences.a
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[ 95%] Building CXX object absl/random/CMakeFiles/random_internal_distribution_test_util.dir/internal/chi_square.cc.o
[ 95%] Building CXX object absl/random/CMakeFiles/random_internal_distribution_test_util.dir/internal/distribution_test_util.cc.o
[ 96%] Linking CXX static library libabsl_random_internal_distribution_test_util.a
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[ 97%] Building CXX object absl/status/CMakeFiles/status.dir/status.cc.o
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[ 99%] Building CXX object absl/types/CMakeFiles/bad_any_cast_impl.dir/bad_any_cast.cc.o
[100%] Linking CXX static library libabsl_bad_any_cast_impl.a
[100%] Built target bad_any_cast_impl
[ 14%] Performing install step for 'abseil'
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Consolidate compiler generated dependencies of target leak_check_disable
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Consolidate compiler generated dependencies of target failure_signal_handler
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[ 64%] Built target bad_variant_access
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Consolidate compiler generated dependencies of target city
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Consolidate compiler generated dependencies of target random_internal_platform
[ 83%] Built target random_internal_platform
Consolidate compiler generated dependencies of target random_internal_randen_hwaes_impl
[ 84%] Built target random_internal_randen_hwaes_impl
Consolidate compiler generated dependencies of target random_internal_randen_hwaes
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[ 87%] Built target random_internal_seed_material
Consolidate compiler generated dependencies of target random_internal_randen_slow
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Consolidate compiler generated dependencies of target random_seed_gen_exception
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Consolidate compiler generated dependencies of target random_internal_randen
[ 90%] Built target random_internal_randen
Consolidate compiler generated dependencies of target random_internal_pool_urbg
[ 91%] Built target random_internal_pool_urbg
Consolidate compiler generated dependencies of target random_distributions
[ 93%] Built target random_distributions
Consolidate compiler generated dependencies of target random_seed_sequences
[ 94%] Built target random_seed_sequences
Consolidate compiler generated dependencies of target random_internal_distribution_test_util
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Install the project...
-- Install configuration: ""
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/cmake/absl/abslTargets.cmake
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/cmake/absl/abslTargets-noconfig.cmake
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/cmake/absl/abslConfig.cmake
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/cmake/absl/abslConfigVersion.cmake
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/algorithm
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/algorithm/algorithm.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/algorithm/container.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/attributes.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/call_once.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/casts.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/config.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/const_init.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/dynamic_annotations.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/atomic_hook.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/atomic_hook_test_helper.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/cycleclock.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/direct_mmap.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/dynamic_annotations.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/endian.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/errno_saver.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/exception_safety_testing.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/exception_testing.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/exponential_biased.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/fast_type_id.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/hide_ptr.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/identity.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/inline_variable.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/inline_variable_testing.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/invoke.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/low_level_alloc.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/low_level_scheduling.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/per_thread_tls.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/periodic_sampler.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/pretty_function.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/raw_logging.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/scheduling_mode.h
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/absl/base/internal/scoped_set_env.h
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-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_hash_policy_traits.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_hashtablez_sampler.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_hashtablez_sampler.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_hashtable_debug.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_hashtable_debug_hooks.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_have_sse.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_node_hash_policy.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_raw_hash_map.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_container_common.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_raw_hash_set.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_raw_hash_set.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_layout.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_stacktrace.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_stacktrace.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_symbolize.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_symbolize.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_examine_stack.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_examine_stack.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_failure_signal_handler.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_failure_signal_handler.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_debugging_internal.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_debugging_internal.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_demangle_internal.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_demangle_internal.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_leak_check.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_leak_check.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_leak_check_disable.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_leak_check_disable.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_debugging.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_flags_path_util.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_flags_program_name.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_flags_program_name.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_flags_config.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_flags_config.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_flags_marshalling.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_flags_marshalling.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_flags_commandlineflag_internal.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_flags_commandlineflag_internal.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_flags_commandlineflag.pc
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-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_flags_private_handle_accessor.pc
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-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_meta.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_bits.pc
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-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_int128.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_numeric.pc
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-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_random.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_bit_gen_ref.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_mock_helpers.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_distributions.pc
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-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_seed_gen_exception.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_random_seed_gen_exception.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_seed_sequences.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_random_seed_sequences.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_traits.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_distribution_caller.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_fast_uniform_bits.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_seed_material.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_random_internal_seed_material.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_pool_urbg.pc
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-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_salted_seed_seq.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_iostream_state_saver.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_generate_real.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_wide_multiply.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_fastmath.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_nonsecure_base.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_pcg_engine.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_randen_engine.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_platform.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_random_internal_platform.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_randen.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_random_internal_randen.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_randen_slow.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_random_internal_randen_slow.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_randen_hwaes.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_random_internal_randen_hwaes.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_randen_hwaes_impl.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_random_internal_randen_hwaes_impl.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_distribution_test_util.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_random_internal_distribution_test_util.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_random_internal_uniform_helper.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_status.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_status.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_statusor.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_statusor.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_strings.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_strings.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_strings_internal.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_strings_internal.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_str_format.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_str_format_internal.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_str_format_internal.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_cord.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_cord.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_graphcycles_internal.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_graphcycles_internal.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_kernel_timeout_internal.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_synchronization.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_synchronization.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_time.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_time.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_civil_time.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_civil_time.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_time_zone.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_time_zone.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_any.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_bad_any_cast.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_bad_any_cast_impl.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_bad_any_cast_impl.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_span.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_optional.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_bad_optional_access.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_bad_optional_access.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_bad_variant_access.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libabsl_bad_variant_access.a
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_variant.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_compare.pc
-- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/absl_utility.pc
[ 16%] Completed 'abseil'
[ 16%] Built target abseil
[ 18%] Creating directories for 'googletest'
[ 20%] Performing download step (git clone) for 'googletest'
Cloning into 'googletest'...
HEAD is now at 703bd9c... Googletest export
[ 22%] No update step for 'googletest'
[ 24%] No patch step for 'googletest'
[ 26%] Performing configure step for 'googletest'
CMake Deprecation Warning at CMakeLists.txt:4 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument
-- The C compiler identification is GNU 9.3.0 -- The CXX compiler identification is GNU 9.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/bin/x86_64-conda-linux-gnu-cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/bin/x86_64-conda-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at googlemock/CMakeLists.txt:45 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.
Update the VERSION argument
CMake Deprecation Warning at googletest/CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.
Update the VERSION argument
-- Found PythonInterp: /home/hchetia/scratch/miniconda3/envs/exphuntermodified/bin/python (found version "3.9.6")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/googletest-prefix/src/googletest-build
[ 28%] Performing build step for 'googletest'
[ 12%] Building CXX object googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
[ 25%] Linking CXX static library ../lib/libgtest.a
[ 25%] Built target gtest
[ 37%] Building CXX object googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o
[ 50%] Linking CXX static library ../lib/libgmock.a
[ 50%] Built target gmock
[ 62%] Building CXX object googlemock/CMakeFiles/gmock_main.dir/src/gmock_main.cc.o
[ 75%] Linking CXX static library ../lib/libgmock_main.a
[ 75%] Built target gmock_main
[ 87%] Building CXX object googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[100%] Linking CXX static library ../lib/libgtest_main.a
[100%] Built target gtest_main
[ 30%] Performing install step for 'googletest'
Consolidate compiler generated dependencies of target gtest
[ 25%] Built target gtest
Consolidate compiler generated dependencies of target gmock
[ 50%] Built target gmock
Consolidate compiler generated dependencies of target gmock_main
[ 75%] Built target gmock_main
Consolidate compiler generated dependencies of target gtest_main
[100%] Built target gtest_main
Install the project...
-- Install configuration: ""
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[ 32%] Completed 'googletest'
[ 32%] Built target googletest
[ 34%] Creating directories for 'htslib'
[ 36%] Performing download step (git clone) for 'htslib'
-- htslib download command succeeded. See also /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/htslib-prefix/src/htslib-stamp/htslib-download-*.log
[ 38%] No update step for 'htslib'
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[ 44%] Performing build step for 'htslib'
bgzf.c:38:10: fatal error: zlib.h: No such file or directory
38 | #include ~~~
compilation terminated.
make[3]: [bgzf.o] Error 1
make[2]: [htslib-prefix/src/htslib-stamp/htslib-build] Error 2
make[1]: [CMakeFiles/htslib.dir/all] Error 2
make: [all] Error 2`
I am also sharing the build folder here. build.zip
Best, Hasna
Thanks,
For the centos7 build it looks like you need to add the zlib-devel
package (see updated installation details here: https://github.com/Illumina/ExpansionHunter/blob/master/docs/02_Installation.md). That shouldn't have passed the cmake configuration step so that is something we can look into.
I see now that the other error you're describing is for macOS w/ gcc10. This would be a tricky case to support. Does the build work for you with the default macOS compiler?
Thanks,
For the centos7 build it looks like you need to add the
zlib-devel
package (see updated installation details here: https://github.com/Illumina/ExpansionHunter/blob/master/docs/02_Installation.md). That shouldn't have passed the cmake configuration step so that is something we can look into.I see now that the other error you're describing is for macOS w/ gcc10. This would be a tricky case to support. Does the build work for you with the default macOS compiler?
Hi @ctsa Thanks. If my build works for centos, then I don't need to make it work for MacOs. I just tried rebuilding with https://anaconda.org/anaconda/zlib-devel-amzn2-aarch64 package, but it didn't work. Could you suggest a way to install zlib-devel without admin privileges?
Hi @ctsa I just installed zlib-devel manually (zlib-devel-1.2.7-19.el7_9.x86_64.rpm). The dir structure is as following-
How can I specify it to the cmake command for Exp-hunter 5.0?
It doesn't appear that the build system has been setup to support alt zlib path for the cmake configuration, @egor-dolzhenko can perhaps confirm this. I do see that other zlib checks were passing in cmake before the error and this was just an issue with htslib, so it suggests some path/env failing to transmit down to htslib in this case.
To give you another option, I just pushed the docker script I used to build the linux release binary here:
https://github.com/Illumina/ExpansionHunter/tree/master/tools/docker/deployment/centos7gcc9src
You can run that anywhere you have docker+root and then copy the binary onto the centos7 system you're trying to work with.
hi @ctsa could you please guide me on how to use the docker version? I installed docker and created a machine "mycontainer". Then I cd'd to the exphunter directory with the shell script and ran exec setup-docker-image-and-build.sh
and got the foll. error-
zsh: command not found: setup-docker-image-and-build.sh
Might be a rookie mistake, I am not a docker user!!
Note the script name ends in .bash
. Also the curdir might not be in your path, so something like this might be more reliable:
bash ./setup-docker-image-and-build.bash
Running bash ./setup-docker-image-and-build.bash gives rise to this error-
Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?
It doesn't look like the docker setup is finished on your system, not sure if you've been able to run any test docker builds before trying this script?
To give you another option, I just pushed the docker script I used to build the linux release binary here:
https://github.com/Illumina/ExpansionHunter/tree/master/tools/docker/deployment/centos7gcc9src
You can run that anywhere you have docker+root and then copy the binary onto the centos7 system you're trying to work with.
Hi @ctsa @egor-dolzhenko I was able to run the docker script that you shared in my macos big sur system with the foll. error-
It doesn't appear that the build system has been setup to support alt zlib path for the cmake configuration, @egor-dolzhenko can perhaps confirm this. I do see that other zlib checks were passing in cmake before the error and this was just an issue with htslib, so it suggests some path/env failing to transmit down to htslib in this case.
My original issue was related to be able to build EH 5.0 from source with my own parameters. Could you please help resolve this?
We've seen this docker error when the host restricts the docker memory to too low of value. On macOS docker desktop comes with a default 2Gb restriction. which seems to be too low for this particular Dockerfile/build script - if you set this to 6Gb I've observed that it works.
I extended the memory and recompiled it with 8 GB. Now the error is different.
How should I proceed with the cmake for building the tool? For example, If I were to proceed with placing a request to my sysadmins to install zlib-devel for me, which specific zlib-devel version should I make the request? My OS is CentOS Linux release 7.9.2009 (Core).
The docker setup script may be assuming that the cwd is the same as the script directory, if you aren't already doing so, then cd to the script directory before running it.
If you're asking an admin to add packages to centos7, and you've already taken care of git, cmake and gcc9 yourself, then the packages listed in the Dockerfile should cover everything else:
bzip2-devel \
libcurl-devel \
libstdc++-static \
xz-devel \
zlib-devel
If you don't want to have to bring your own newer gcc version, you can also ask them if they would install devtoolset-9.
Hi Egor, I am trying to compile Expn hunter, with some modifications to its source code, in a conda environment. GCC version- 9.3.0 In CentOS Linux release 7.9.2009 (Core)
In file included from bgzf.c:39: htslib/bgzf.h:34:10: fatal error: zlib.h: No such file or directory 34 | #include
| ^
~~~ compilation terminated. make[3]: [bgzf.o] Error 1 make[2]: [thirdparty/htslib/src/htslib-stamp/htslib-build] Error 2 make[1]: [CMakeFiles/htslib.dir/all] Error 2 make: [all] Error 2 (exphuntermodified) [hchetia@nhgalaxy3 build]$ ggc -version bash: ggc: command not found... (exphuntermodified) [hchetia@nhgalaxy3 build]$ gcc -version gcc: error: unrecognized command line option '-version' gcc: fatal error: no input files compilation terminated.Regards, Hasna