Error compiling Expansion Hunter

hchetia commented 2 years ago

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

hchetia commented 2 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

egor-dolzhenko commented 2 years ago

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

egor-dolzhenko commented 2 years ago

@hchetia, the new version was just released. Could you please check if you can build the new version?

hchetia commented 2 years ago

Hi Egor,

Thanks for the new release. Let me try building and get back to you! Best, Hasna

hchetia commented 2 years ago

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

ctsa commented 2 years ago

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?

hchetia commented 2 years ago

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' [ 1%] Building CXX object absl/base/CMakeFiles/strerror.dir/internal/strerror.cc.o [ 1%] Linking CXX static library libabsl_strerror.a [ 1%] Built target strerror [ 1%] Building CXX object absl/base/CMakeFiles/log_severity.dir/log_severity.cc.o [ 2%] Linking CXX static library libabsl_log_severity.a [ 2%] Built target log_severity [ 2%] Building CXX object absl/base/CMakeFiles/raw_logging_internal.dir/internal/raw_logging.cc.o [ 3%] Linking CXX static library libabsl_raw_logging_internal.a [ 3%] Built target raw_logging_internal [ 3%] Building CXX object absl/base/CMakeFiles/scoped_set_env.dir/internal/scoped_set_env.cc.o [ 4%] Linking CXX static library libabsl_scoped_set_env.a [ 4%] Built target scoped_set_env [ 4%] Building CXX object absl/base/CMakeFiles/exponential_biased.dir/internal/exponential_biased.cc.o [ 5%] Linking CXX static library libabsl_exponential_biased.a [ 5%] Built target exponential_biased [ 6%] Building CXX object absl/base/CMakeFiles/periodic_sampler.dir/internal/periodic_sampler.cc.o [ 6%] Linking CXX static library libabsl_periodic_sampler.a [ 6%] Built target periodic_sampler [ 6%] Building CXX object absl/base/CMakeFiles/spinlock_wait.dir/internal/spinlock_wait.cc.o [ 7%] Linking CXX static library libabsl_spinlock_wait.a [ 7%] Built target spinlock_wait [ 8%] Building CXX object absl/base/CMakeFiles/base.dir/internal/cycleclock.cc.o [ 8%] Building CXX object absl/base/CMakeFiles/base.dir/internal/spinlock.cc.o [ 9%] Building CXX object absl/base/CMakeFiles/base.dir/internal/sysinfo.cc.o [ 9%] Building CXX object absl/base/CMakeFiles/base.dir/internal/thread_identity.cc.o [ 10%] Building CXX object absl/base/CMakeFiles/base.dir/internal/unscaledcycleclock.cc.o [ 11%] Linking CXX static library libabsl_base.a [ 11%] Built target base [ 12%] Building CXX object absl/base/CMakeFiles/malloc_internal.dir/internal/low_level_alloc.cc.o [ 12%] Linking CXX static library libabsl_malloc_internal.a [ 12%] Built target malloc_internal [ 12%] Building CXX object absl/base/CMakeFiles/throw_delegate.dir/internal/throw_delegate.cc.o [ 13%] Linking CXX static library libabsl_throw_delegate.a [ 13%] Built target throw_delegate [ 13%] Building CXX object absl/types/CMakeFiles/bad_optional_access.dir/bad_optional_access.cc.o [ 14%] Linking CXX static library libabsl_bad_optional_access.a [ 14%] Built target bad_optional_access [ 14%] Building CXX object absl/time/CMakeFiles/civil_time.dir/internal/cctz/src/civil_time_detail.cc.o [ 15%] Linking CXX static library libabsl_civil_time.a [ 15%] Built target civil_time [ 16%] Building CXX object absl/numeric/CMakeFiles/int128.dir/int128.cc.o [ 17%] Linking CXX static library libabsl_int128.a [ 17%] Built target int128 [ 17%] Building CXX 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61%] Building CXX object absl/strings/CMakeFiles/str_format_internal.dir/internal/str_format/float_conversion.cc.o [ 61%] Building CXX object absl/strings/CMakeFiles/str_format_internal.dir/internal/str_format/output.cc.o [ 62%] Building CXX object absl/strings/CMakeFiles/str_format_internal.dir/internal/str_format/parser.cc.o [ 62%] Linking CXX static library libabsl_str_format_internal.a [ 62%] Built target str_format_internal [ 63%] Building CXX object absl/flags/CMakeFiles/flags_marshalling.dir/marshalling.cc.o [ 63%] Linking CXX static library libabsl_flags_marshalling.a [ 63%] Built target flags_marshalling [ 63%] Building CXX object absl/types/CMakeFiles/bad_variant_access.dir/bad_variant_access.cc.o [ 64%] Linking CXX static library libabsl_bad_variant_access.a [ 64%] Built target bad_variant_access [ 64%] Building CXX object absl/flags/CMakeFiles/flags_commandlineflag_internal.dir/internal/commandlineflag.cc.o [ 65%] Linking CXX static library 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target flags_usage_internal [ 80%] Building CXX object absl/flags/CMakeFiles/flags_usage.dir/usage.cc.o [ 81%] Linking CXX static library libabsl_flags_usage.a [ 81%] Built target flags_usage [ 82%] Building CXX object absl/flags/CMakeFiles/flags_parse.dir/parse.cc.o [ 82%] Linking CXX static library libabsl_flags_parse.a [ 82%] Built target flags_parse [ 82%] Building CXX object absl/random/CMakeFiles/random_internal_platform.dir/internal/randen_round_keys.cc.o [ 83%] Linking CXX static library libabsl_random_internal_platform.a [ 83%] Built target random_internal_platform [ 83%] Building CXX object absl/random/CMakeFiles/random_internal_randen_hwaes_impl.dir/internal/randen_hwaes.cc.o [ 84%] Linking CXX static library libabsl_random_internal_randen_hwaes_impl.a [ 84%] Built target random_internal_randen_hwaes_impl [ 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 [ 86%] Built target random_internal_randen_hwaes [ 86%] Building CXX object absl/random/CMakeFiles/random_internal_seed_material.dir/internal/seed_material.cc.o [ 87%] Linking CXX static library libabsl_random_internal_seed_material.a [ 87%] Built target random_internal_seed_material [ 87%] Building CXX object absl/random/CMakeFiles/random_internal_randen_slow.dir/internal/randen_slow.cc.o [ 88%] Linking CXX static library libabsl_random_internal_randen_slow.a [ 88%] Built target random_internal_randen_slow [ 89%] Building CXX object absl/random/CMakeFiles/random_seed_gen_exception.dir/seed_gen_exception.cc.o [ 89%] Linking CXX static library libabsl_random_seed_gen_exception.a [ 89%] Built target random_seed_gen_exception [ 90%] Building CXX object absl/random/CMakeFiles/random_internal_randen.dir/internal/randen.cc.o [ 90%] Linking CXX static library libabsl_random_internal_randen.a [ 90%] Built target random_internal_randen [ 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 [ 91%] Built target random_internal_pool_urbg [ 92%] Building CXX object absl/random/CMakeFiles/random_distributions.dir/discrete_distribution.cc.o [ 93%] Building CXX object absl/random/CMakeFiles/random_distributions.dir/gaussian_distribution.cc.o [ 93%] Linking CXX static library libabsl_random_distributions.a [ 93%] Built target random_distributions [ 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 [ 94%] Built target random_seed_sequences [ 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 [ 96%] Built target random_internal_distribution_test_util [ 97%] Building CXX object absl/status/CMakeFiles/status.dir/status.cc.o [ 97%] Building CXX object absl/status/CMakeFiles/status.dir/status_payload_printer.cc.o [ 98%] Linking CXX static library libabsl_status.a [ 98%] Built target status [ 99%] Building CXX object absl/status/CMakeFiles/statusor.dir/statusor.cc.o [ 99%] Linking CXX static library libabsl_statusor.a [ 99%] Built target statusor [ 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' Consolidate compiler generated dependencies of target strerror [ 1%] Built target strerror Consolidate compiler generated dependencies of target log_severity [ 2%] Built target log_severity Consolidate compiler generated dependencies of target raw_logging_internal [ 3%] Built target raw_logging_internal Consolidate compiler generated dependencies of target scoped_set_env [ 4%] Built target scoped_set_env Consolidate compiler generated dependencies of target exponential_biased [ 5%] Built target exponential_biased Consolidate compiler generated dependencies of target periodic_sampler [ 6%] Built target periodic_sampler Consolidate compiler generated dependencies of target spinlock_wait [ 7%] Built target spinlock_wait Consolidate compiler generated dependencies of target base [ 11%] Built target base Consolidate compiler generated dependencies of target malloc_internal [ 12%] Built target malloc_internal Consolidate compiler generated dependencies of target throw_delegate [ 13%] Built target throw_delegate Consolidate compiler generated dependencies of target bad_optional_access [ 14%] Built target bad_optional_access Consolidate compiler generated dependencies of target civil_time [ 15%] Built target civil_time Consolidate compiler generated dependencies of target int128 [ 17%] Built target int128 Consolidate compiler generated dependencies of target strings_internal [ 19%] Built target strings_internal Consolidate compiler generated dependencies of target strings [ 28%] Built target strings Consolidate compiler generated dependencies of target time_zone [ 34%] Built target time_zone Consolidate compiler generated dependencies of target time [ 37%] Built target time Consolidate compiler generated dependencies of target debugging_internal [ 40%] Built target debugging_internal Consolidate compiler generated dependencies of target stacktrace [ 41%] Built target stacktrace Consolidate compiler generated dependencies of target demangle_internal [ 42%] Built target demangle_internal Consolidate compiler generated dependencies of target symbolize [ 43%] Built target symbolize Consolidate compiler generated dependencies of target graphcycles_internal [ 44%] Built target graphcycles_internal Consolidate compiler generated dependencies of target synchronization [ 49%] Built target synchronization Consolidate compiler generated dependencies of target hashtablez_sampler [ 50%] Built target hashtablez_sampler Consolidate compiler generated dependencies of target raw_hash_set [ 52%] Built target raw_hash_set Consolidate compiler generated dependencies of target examine_stack [ 53%] Built target examine_stack Consolidate compiler generated dependencies of target leak_check [ 54%] Built target leak_check Consolidate compiler generated dependencies of target leak_check_disable [ 55%] Built target leak_check_disable Consolidate compiler generated dependencies of target failure_signal_handler [ 56%] Built target failure_signal_handler Consolidate compiler generated dependencies of target flags_program_name [ 57%] Built target flags_program_name Consolidate compiler generated dependencies of target flags_config [ 58%] Built target flags_config Consolidate compiler generated dependencies of target str_format_internal [ 62%] Built target str_format_internal Consolidate compiler generated dependencies of target flags_marshalling [ 63%] Built target flags_marshalling Consolidate compiler generated dependencies of target bad_variant_access [ 64%] Built target bad_variant_access Consolidate compiler generated dependencies of target flags_commandlineflag_internal [ 65%] Built target flags_commandlineflag_internal Consolidate compiler generated dependencies of target flags_commandlineflag [ 67%] Built target flags_commandlineflag Consolidate compiler generated dependencies of target flags_private_handle_accessor [ 69%] Built target flags_private_handle_accessor Consolidate compiler generated dependencies of target wyhash [ 71%] Built target wyhash Consolidate compiler generated dependencies of target city [ 72%] Built target city Consolidate compiler generated dependencies of target hash [ 74%] Built target hash Consolidate compiler generated dependencies of target cord [ 76%] Built target cord Consolidate compiler generated dependencies of target flags_reflection [ 77%] Built target flags_reflection Consolidate compiler generated dependencies of target flags_internal [ 78%] Built target flags_internal Consolidate compiler generated dependencies of target flags [ 79%] Built target flags Consolidate compiler generated dependencies of target flags_usage_internal [ 80%] Built target flags_usage_internal Consolidate compiler generated dependencies of target flags_usage [ 81%] Built target flags_usage Consolidate compiler generated dependencies of target flags_parse [ 82%] Built target flags_parse 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 [ 86%] Built target random_internal_randen_hwaes Consolidate compiler generated dependencies of target random_internal_seed_material [ 87%] Built target random_internal_seed_material Consolidate compiler generated dependencies of target random_internal_randen_slow [ 88%] Built target random_internal_randen_slow Consolidate compiler generated dependencies of target random_seed_gen_exception [ 89%] Built target random_seed_gen_exception 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 [ 96%] Built target random_internal_distribution_test_util Consolidate compiler generated dependencies of target status [ 98%] Built target status Consolidate compiler generated dependencies of target statusor [ 99%] Built target statusor Consolidate compiler generated dependencies of target bad_any_cast_impl [100%] Built target bad_any_cast_impl 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 -- 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/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 value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- 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 value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

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 value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- 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: "" -- Up-to-date: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-actions.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-cardinalities.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-function-mocker.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-generated-actions.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-generated-actions.h.pump -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-generated-function-mockers.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-generated-function-mockers.h.pump -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-generated-matchers.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-generated-matchers.h.pump -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-matchers.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-more-actions.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-more-matchers.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-nice-strict.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock-spec-builders.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/gmock.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal/custom -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal/custom/README.md -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal/custom/gmock-generated-actions.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal/custom/gmock-generated-actions.h.pump -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal/custom/gmock-matchers.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal/custom/gmock-port.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal/gmock-internal-utils.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal/gmock-port.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gmock/internal/gmock-pp.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libgmock.a -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libgmock_main.a -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/gmock.pc -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/gmock_main.pc -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/cmake/GTest/GTestTargets.cmake -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/cmake/GTest/GTestTargets-noconfig.cmake -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/cmake/GTest/GTestConfigVersion.cmake -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/cmake/GTest/GTestConfig.cmake -- Up-to-date: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest-death-test.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest-matchers.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest-message.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest-param-test.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest-printers.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest-spi.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest-test-part.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest-typed-test.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest_pred_impl.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/gtest_prod.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/custom -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/custom/README.md -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/custom/gtest-port.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/custom/gtest-printers.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/custom/gtest.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/gtest-death-test-internal.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/gtest-filepath.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/gtest-internal.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/gtest-param-util.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/gtest-port-arch.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/gtest-port.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/gtest-string.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/gtest-type-util.h -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/include/gtest/internal/gtest-type-util.h.pump -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libgtest.a -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/libgtest_main.a -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/gtest.pc -- Installing: /home/hchetia/scratch/softwares/ExpansionHunter-5.0.0/build/install/lib64/pkgconfig/gtest_main.pc [ 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' [ 40%] No patch step for 'htslib' [ 42%] No configure step for 'htslib' [ 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

ctsa commented 2 years ago

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?

hchetia commented 2 years ago

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?

hchetia commented 2 years ago

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?

ctsa commented 2 years ago

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.

ctsa commented 2 years ago

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.

hchetia commented 2 years ago

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!!

ctsa commented 2 years ago

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

hchetia commented 2 years ago

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?

ctsa commented 2 years ago

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?

hchetia commented 2 years ago

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?

ctsa commented 2 years ago

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.

hchetia commented 2 years ago

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).

ctsa commented 2 years ago

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.

Illumina / ExpansionHunter

Error compiling Expansion Hunter #138