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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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EHv4 link error on MacOSX: "Undefined symbols for architecture x86_64: "testing::internal::g_linked_ptr_mutex" #108

Closed bw2 closed 3 years ago

bw2 commented 3 years ago

On MacOSX I'm seeing this link error when building master:

wm4d1-03b:~/p1/bin/ExpansionHunter-repo/build $ cmake ..
-- Configuring done
-- Generating done
-- Build files have been written to: ~/project1/bin/ExpansionHunter-repo/build/googletest-download
[ 11%] Performing update step for 'googletest'
[ 22%] No patch step for 'googletest'
[ 33%] No configure step for 'googletest'
[ 44%] No build step for 'googletest'
[ 55%] No install step for 'googletest'
[ 66%] No test step for 'googletest'
[ 77%] Completed 'googletest'
[100%] Built target googletest
-- Found Boost: /usr/local/lib/cmake/Boost-1.73.0/BoostConfig.cmake (found suitable version "1.73.0", minimum required is "1.4") found components: program_options filesystem regex date_time system
-- Found Boost: /usr/local/lib/cmake/Boost-1.73.0/BoostConfig.cmake (found suitable version "1.73.0", minimum required is "1.5") found components: program_options filesystem system
-- Configuring done
-- Generating done
-- Build files have been written to: ~/p1/bin/ExpansionHunter-repo/build

wm4d1-03b:~/p1/bin/ExpansionHunter-repo/build $ make
Scanning dependencies of target zlib
[  1%] Creating directories for 'zlib'
[  1%] Performing download step (git clone) for 'zlib'
-- zlib download command succeeded.  See also ~/p1/bin/ExpansionHunter-repo/build/thirdparty/zlib/src/zlib-stamp/zlib-download-*.log
[  2%] No update step for 'zlib'
[  2%] No patch step for 'zlib'
[  3%] Performing configure step for 'zlib'
Checking for gcc...
Building static library libz.a version 1.2.8 with gcc.
Checking for off64_t... No.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
[  4%] Performing build step for 'zlib'
inflate.c:1507:61: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
    if (strm == Z_NULL || strm->state == Z_NULL) return -1L << 16;
                                                        ~~~ ^
1 warning generated.
[  4%] Performing install step for 'zlib'
-- zlib install command succeeded.  See also ~/p1/bin/ExpansionHunter-repo/build/thirdparty/zlib/src/zlib-stamp/zlib-install-*.log
[  5%] Completed 'zlib'
[  5%] Built target zlib
Scanning dependencies of target htslib
[  6%] Creating directories for 'htslib'
[  6%] Performing download step (git clone) for 'htslib'
-- htslib download command succeeded.  See also ~/p1/bin/ExpansionHunter-repo/build/thirdparty/htslib/src/htslib-stamp/htslib-download-*.log
[  7%] No update step for 'htslib'
[  7%] No patch step for 'htslib'
[  8%] No configure step for 'htslib'
[  8%] Performing build step for 'htslib'
hts.c:48:5: warning: unused function 'ks_getc' [-Wunused-function]
    KSTREAM_INIT2(, BGZF*, bgzf_read, 65536)
    ^
./htslib/kseq.h:152:2: note: expanded from macro 'KSTREAM_INIT2'
        __KS_INLINED(__read)
        ^
./htslib/kseq.h:68:20: note: expanded from macro '__KS_INLINED'
        static inline int ks_getc(kstream_t *ks) \
                          ^
1 warning generated.
cram/cram_io.c:3096:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:311: note: expanded from macro 'itf8_put'
  ...=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
     ~~~~~^~~~~~~~~~~~~~~~~
cram/cram_io.c:3096:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:345: note: expanded from macro 'itf8_put'
  ...=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
     ~~~~~~~~~~^~~~~
cram/cram_io.c:3096:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:367: note: expanded from macro 'itf8_put'
  ...=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
     ~~~~~~~~~~^~~~~
cram/cram_io.c:3096:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:388: note: expanded from macro 'itf8_put'
  ...=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
     ~~~~~~~~~^~~~~
cram/cram_io.c:3154:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:311: note: expanded from macro 'itf8_put'
  ...=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
     ~~~~~^~~~~~~~~~~~~~~~~
cram/cram_io.c:3154:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:345: note: expanded from macro 'itf8_put'
  ...=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
     ~~~~~~~~~~^~~~~
cram/cram_io.c:3154:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:367: note: expanded from macro 'itf8_put'
  ...=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
     ~~~~~~~~~~^~~~~
cram/cram_io.c:3154:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
        cp += itf8_put(cp, -2);
              ^~~~~~~~~~~~~~~~
cram/cram_io.h:97:388: note: expanded from macro 'itf8_put'
  ...=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
     ~~~~~~~~~^~~~~
8 warnings generated.
[  8%] Performing install step for 'htslib'
[  9%] Completed 'htslib'
[  9%] Built target htslib
Scanning dependencies of target graphtools
[ 10%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/GaplessAligner.cpp.o
[ 10%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/GappedAligner.cpp.o
[ 11%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/GraphAlignment.cpp.o
[ 11%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/GraphAlignmentOperations.cpp.o
[ 12%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/KmerIndex.cpp.o
[ 12%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/KmerIndexOperations.cpp.o
[ 13%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/LinearAlignment.cpp.o
[ 13%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/LinearAlignmentOperations.cpp.o
[ 14%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/Operation.cpp.o
[ 15%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/OperationOperations.cpp.o
[ 15%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/PinnedAligner.cpp.o
[ 16%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/TracebackMatrix.cpp.o
[ 16%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/TracebackRunner.cpp.o
[ 17%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphalign/dagAligner/PenaltyMatrix.cpp.o
[ 17%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphcore/Graph.cpp.o
[ 18%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphcore/GraphBuilders.cpp.o
[ 18%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphcore/GraphCoordinates.cpp.o
[ 19%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphcore/GraphOperations.cpp.o
[ 19%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphcore/GraphReferenceMapping.cpp.o
[ 20%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphcore/Path.cpp.o
[ 21%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphcore/PathFamily.cpp.o
[ 21%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphcore/PathFamilyOperations.cpp.o
[ 22%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphcore/PathOperations.cpp.o
[ 22%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphio/AlignmentWriter.cpp.o
[ 23%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphio/GraphJson.cpp.o
[ 23%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphutils/DepthTest.cpp.o
[ 24%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphutils/IntervalBuffer.cpp.o
[ 24%] Building CXX object thirdparty/graph-tools-master/CMakeFiles/graphtools.dir/src/graphutils/SequenceOperations.cpp.o
[ 25%] Linking CXX static library libgraphtools.a
[ 25%] Built target graphtools
Scanning dependencies of target region_spec
[ 25%] Building CXX object region_spec/CMakeFiles/region_spec.dir/LocusSpecification.cpp.o
[ 26%] Building CXX object region_spec/CMakeFiles/region_spec.dir/VariantSpecification.cpp.o
[ 27%] Linking CXX static library libregion_spec.a
[ 27%] Built target region_spec
Scanning dependencies of target common
[ 28%] Building CXX object common/CMakeFiles/common.dir/Common.cpp.o
[ 29%] Building CXX object common/CMakeFiles/common.dir/CountTable.cpp.o
[ 29%] Building CXX object common/CMakeFiles/common.dir/GenomicRegion.cpp.o
[ 30%] Building CXX object common/CMakeFiles/common.dir/HtsHelpers.cpp.o
[ 30%] Building CXX object common/CMakeFiles/common.dir/Parameters.cpp.o
[ 31%] Building CXX object common/CMakeFiles/common.dir/Reference.cpp.o
[ 31%] Building CXX object common/CMakeFiles/common.dir/ReferenceContigInfo.cpp.o
[ 32%] Linking CXX static library libcommon.a
[ 32%] Built target common
Scanning dependencies of target filtering
[ 32%] Building CXX object filtering/CMakeFiles/filtering.dir/GraphVariantAlignmentStats.cpp.o
[ 33%] Building CXX object filtering/CMakeFiles/filtering.dir/OrientationPredictor.cpp.o
[ 33%] Linking CXX static library libfiltering.a
[ 33%] Built target filtering
Scanning dependencies of target stats
[ 34%] Building CXX object stats/CMakeFiles/stats.dir/LocusStats.cpp.o
[ 34%] Building CXX object stats/CMakeFiles/stats.dir/ReadSupportCalculator.cpp.o
[ 35%] Building CXX object stats/CMakeFiles/stats.dir/WeightedPurityCalculator.cpp.o
[ 35%] Linking CXX static library libstats.a
[ 35%] Built target stats
Scanning dependencies of target input
[ 36%] Building CXX object input/CMakeFiles/input.dir/CatalogLoading.cpp.o
[ 37%] Building CXX object input/CMakeFiles/input.dir/GraphBlueprint.cpp.o
[ 37%] Building CXX object input/CMakeFiles/input.dir/LocusSpecDecoding.cpp.o
[ 38%] Building CXX object input/CMakeFiles/input.dir/ParameterLoading.cpp.o
[ 38%] Building CXX object input/CMakeFiles/input.dir/RegionGraph.cpp.o
[ 39%] Building CXX object input/CMakeFiles/input.dir/SampleStats.cpp.o
[ 39%] Linking CXX static library libinput.a
[ 39%] Built target input
Scanning dependencies of target genotyping
[ 40%] Building CXX object genotyping/CMakeFiles/genotyping.dir/AlignMatrix.cpp.o
[ 41%] Building CXX object genotyping/CMakeFiles/genotyping.dir/AlleleChecker.cpp.o
[ 41%] Building CXX object genotyping/CMakeFiles/genotyping.dir/RepeatGenotype.cpp.o
[ 42%] Building CXX object genotyping/CMakeFiles/genotyping.dir/SmallVariantGenotype.cpp.o
[ 42%] Building CXX object genotyping/CMakeFiles/genotyping.dir/SmallVariantGenotyper.cpp.o
[ 43%] Building CXX object genotyping/CMakeFiles/genotyping.dir/StrAlign.cpp.o
[ 43%] Building CXX object genotyping/CMakeFiles/genotyping.dir/OneAlleleStrGenotyper.cpp.o
[ 44%] Building CXX object genotyping/CMakeFiles/genotyping.dir/TwoAlleleStrGenotyper.cpp.o
[ 44%] Building CXX object genotyping/CMakeFiles/genotyping.dir/FragLogliks.cpp.o
[ 45%] Building CXX object genotyping/CMakeFiles/genotyping.dir/StrGenotyper.cpp.o
[ 45%] Building CXX object genotyping/CMakeFiles/genotyping.dir/AlignMatrixFiltering.cpp.o
[ 46%] Linking CXX static library libgenotyping.a
[ 46%] Built target genotyping
Scanning dependencies of target reads
[ 47%] Building CXX object reads/CMakeFiles/reads.dir/Read.cpp.o
[ 48%] Building CXX object reads/CMakeFiles/reads.dir/ReadPairs.cpp.o
[ 48%] Linking CXX static library libreads.a
[ 48%] Built target reads
Scanning dependencies of target classification
[ 48%] Building CXX object classification/CMakeFiles/classification.dir/AlignmentClassifier.cpp.o
[ 49%] Building CXX object classification/CMakeFiles/classification.dir/ClassifierOfAlignmentsToVariant.cpp.o
[ 49%] Linking CXX static library libclassification.a
[ 49%] Built target classification
Scanning dependencies of target alignment
[ 50%] Building CXX object alignment/CMakeFiles/alignment.dir/AlignmentFilters.cpp.o
[ 50%] Building CXX object alignment/CMakeFiles/alignment.dir/AlignmentTweakers.cpp.o
[ 51%] Building CXX object alignment/CMakeFiles/alignment.dir/GreedyAlignmentIntersector.cpp.o
[ 51%] Building CXX object alignment/CMakeFiles/alignment.dir/HighQualityBaseRunFinder.cpp.o
[ 52%] Building CXX object alignment/CMakeFiles/alignment.dir/OperationsOnAlignments.cpp.o
[ 52%] Building CXX object alignment/CMakeFiles/alignment.dir/SoftclippingAligner.cpp.o
[ 53%] Linking CXX static library libalignment.a
[ 53%] Built target alignment
Scanning dependencies of target region_analysis
[ 54%] Building CXX object region_analysis/CMakeFiles/region_analysis.dir/LocusAnalyzer.cpp.o
[ 54%] Building CXX object region_analysis/CMakeFiles/region_analysis.dir/LocusFindings.cpp.o
[ 55%] Building CXX object region_analysis/CMakeFiles/region_analysis.dir/RepeatAnalyzer.cpp.o
[ 55%] Building CXX object region_analysis/CMakeFiles/region_analysis.dir/SmallVariantAnalyzer.cpp.o
[ 56%] Building CXX object region_analysis/CMakeFiles/region_analysis.dir/VariantAnalyzer.cpp.o
[ 56%] Building CXX object region_analysis/CMakeFiles/region_analysis.dir/VariantFindings.cpp.o
[ 57%] Linking CXX static library libregion_analysis.a
[ 57%] Built target region_analysis
Scanning dependencies of target sample_analysis
[ 57%] Building CXX object sample_analysis/CMakeFiles/sample_analysis.dir/AnalyzerFinder.cpp.o
[ 58%] Building CXX object sample_analysis/CMakeFiles/sample_analysis.dir/GenomeMask.cpp.o
[ 58%] Building CXX object sample_analysis/CMakeFiles/sample_analysis.dir/GenomeQueryCollection.cpp.o
[ 59%] Building CXX object sample_analysis/CMakeFiles/sample_analysis.dir/HtsFileSeeker.cpp.o
[ 59%] Building CXX object sample_analysis/CMakeFiles/sample_analysis.dir/HtsFileStreamer.cpp.o
[ 60%] Building CXX object sample_analysis/CMakeFiles/sample_analysis.dir/HtsSeekingSampleAnalysis.cpp.o
[ 60%] Building CXX object sample_analysis/CMakeFiles/sample_analysis.dir/HtsStreamingSampleAnalysis.cpp.o
[ 61%] Building CXX object sample_analysis/CMakeFiles/sample_analysis.dir/IndexBasedDepthEstimate.cpp.o
[ 61%] Building CXX object sample_analysis/CMakeFiles/sample_analysis.dir/MateExtractor.cpp.o
[ 62%] Linking CXX static library libsample_analysis.a
[ 62%] Built target sample_analysis
Scanning dependencies of target output
[ 63%] Building CXX object output/CMakeFiles/output.dir/BamletWriter.cpp.o
[ 63%] Building CXX object output/CMakeFiles/output.dir/JsonWriter.cpp.o
[ 64%] Building CXX object output/CMakeFiles/output.dir/VcfHeader.cpp.o
[ 64%] Building CXX object output/CMakeFiles/output.dir/VcfWriter.cpp.o
[ 65%] Building CXX object output/CMakeFiles/output.dir/VcfWriterHelpers.cpp.o
[ 65%] Linking CXX static library liboutput.a
[ 65%] Built target output
Scanning dependencies of target ExpansionHunter
[ 66%] Building CXX object CMakeFiles/ExpansionHunter.dir/src/ExpansionHunter.cpp.o
[ 66%] Linking CXX executable ExpansionHunter
ld: warning: direct access in function 'boost::wrapexcept<boost::program_options::validation_error>::rethrow() const' from file '/usr/local/lib/libboost_program_options-mt.a(value_semantic.o)' to global weak symbol 'typeinfo for boost::wrapexcept<boost::program_options::validation_error>' from file 'input/libinput.a(ParameterLoading.cpp.o)' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in function 'boost::filesystem::detail::directory_iterator_construct(boost::filesystem::directory_iterator&, boost::filesystem::path const&, unsigned int, boost::system::error_code*)' from file '/usr/local/lib/libboost_filesystem-mt.a(directory.o)' to global weak symbol 'boost::system::detail::is_generic_value(int)::gen' from file 'input/libinput.a(SampleStats.cpp.o)' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in function 'boost::system::detail::system_error_category::default_error_condition(int) const' from file '/usr/local/lib/libboost_filesystem-mt.a(operations.o)' to global weak symbol 'boost::system::detail::is_generic_value(int)::gen' from file 'input/libinput.a(SampleStats.cpp.o)' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
[ 66%] Built target ExpansionHunter
Scanning dependencies of target gtest
[ 66%] Building CXX object googletest-build/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
[ 67%] Linking CXX static library ../../lib/libgtest.a
[ 67%] Built target gtest
Scanning dependencies of target gmock
[ 68%] Building CXX object googletest-build/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o
[ 68%] Linking CXX static library ../../lib/libgmock.a
[ 68%] Built target gmock
Scanning dependencies of target gmock_main
[ 69%] Building CXX object googletest-build/googlemock/CMakeFiles/gmock_main.dir/src/gmock_main.cc.o
[ 69%] Linking CXX static library ../../lib/libgmock_main.a
[ 69%] Built target gmock_main
Scanning dependencies of target gtest_main
[ 70%] Building CXX object googletest-build/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[ 70%] Linking CXX static library ../../lib/libgtest_main.a
[ 70%] Built target gtest_main
Scanning dependencies of target GenomicRegionTest
[ 71%] Building CXX object common/tests/CMakeFiles/GenomicRegionTest.dir/GenomicRegionTest.cpp.o
[ 71%] Linking CXX executable GenomicRegionTest
[ 71%] Built target GenomicRegionTest
Scanning dependencies of target CountTableTest
[ 71%] Building CXX object common/tests/CMakeFiles/CountTableTest.dir/CountTableTest.cpp.o
[ 72%] Linking CXX executable CountTableTest
[ 72%] Built target CountTableTest
Scanning dependencies of target StrGenotyperTest
[ 72%] Building CXX object genotyping/tests/CMakeFiles/StrGenotyperTest.dir/StrGenotyperTest.cpp.o
[ 73%] Linking CXX executable StrGenotyperTest
[ 73%] Built target StrGenotyperTest
Scanning dependencies of target RepeatGenotypeTest
[ 74%] Building CXX object genotyping/tests/CMakeFiles/RepeatGenotypeTest.dir/RepeatGenotypeTest.cpp.o
[ 75%] Linking CXX executable RepeatGenotypeTest
[ 75%] Built target RepeatGenotypeTest
Scanning dependencies of target StrAlignMatrixTest
[ 75%] Building CXX object genotyping/tests/CMakeFiles/StrAlignMatrixTest.dir/AlignMatrixTest.cpp.o
[ 76%] Linking CXX executable StrAlignMatrixTest
[ 76%] Built target StrAlignMatrixTest
Scanning dependencies of target StrAlignTest
[ 76%] Building CXX object genotyping/tests/CMakeFiles/StrAlignTest.dir/StrAlignTest.cpp.o
[ 77%] Linking CXX executable StrAlignTest
[ 77%] Built target StrAlignTest
Scanning dependencies of target AlleleCheckerTest
[ 77%] Building CXX object genotyping/tests/CMakeFiles/AlleleCheckerTest.dir/AlleleCheckerTest.cpp.o
[ 78%] Linking CXX executable AlleleCheckerTest
[ 78%] Built target AlleleCheckerTest
Scanning dependencies of target FragLogliksTest
[ 79%] Building CXX object genotyping/tests/CMakeFiles/FragLogliksTest.dir/FragLogliksTest.cpp.o
[ 79%] Linking CXX executable FragLogliksTest
Undefined symbols for architecture x86_64:
  "testing::internal::g_linked_ptr_mutex", referenced from:
      testing::internal::linked_ptr_internal::depart() in FragLogliksTest.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [genotyping/tests/FragLogliksTest] Error 1
make[1]: *** [genotyping/tests/CMakeFiles/FragLogliksTest.dir/all] Error 2
make: *** [all] Error 2

wm4d1-03b:~/p1/bin/ExpansionHunter-repo/build $ cd ..
wm4d1-03b:~/p1/bin/ExpansionHunter-repo $ git pull
Already up to date.
wm4d1-03b:~/p1/bin/ExpansionHunter-repo $ cmake --version
cmake version 3.18.2

CMake suite maintained and supported by Kitware (kitware.com/cmake).
wm4d1-03b:~/p1/bin/ExpansionHunter-repo $ gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.3 (clang-1103.0.32.62)
Target: x86_64-apple-darwin19.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
bw2 commented 3 years ago

Using provided binaries instead.

YuwenZhao-tian commented 2 years ago

Hi I have encountered this same error. May I ask how to use provided binaries?

egor-dolzhenko commented 2 years ago

Thanks for the question @YuwenZhao-tian! The binaries can be found under "Assets" on the release page: https://github.com/Illumina/ExpansionHunter/releases/tag/v5.0.0

Please let us know if you have any issues with using these binaries.