Compile failure on Mac OS Mojave

Question

Compile failure on Mac OS Mojave

pbpearman opened this issue 5 years ago · 1 comments

Hello Gabriel,
Here is the compilation output I get when I tried to compile on Mac Mojave v. 10.14.4
Peter

uhtred:glactools-master bgppermp$ make
rm -rf bamtools/
git clone --recursive https://github.com/pezmaster31/bamtools.git
Cloning into 'bamtools'...
remote: Enumerating objects: 4857, done.
remote: Total 4857 (delta 0), reused 0 (delta 0), pack-reused 4857
Receiving objects: 100% (4857/4857), 6.06 MiB | 8.05 MiB/s, done.
Resolving deltas: 100% (3373/3373), done.
cd bamtools/ && mkdir -p build/ && cd build/ && cmake .. && make && cd ../..
-- The CXX compiler identification is AppleClang 10.0.1.10010046
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at CMakeLists.txt:20 (cmake_policy):
The OLD behavior for policy CMP0042 will be removed from a future version
of CMake.

The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.

-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")
-- Checking for one of the modules 'jsoncpp>=1'
Did NOT find system JsonCpp, instead using bundled version
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.11")
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/bgppermp/Downloads/glactools-master/bamtools/build
Scanning dependencies of target SharedHeaders
[ 0%] Built target SharedHeaders
Scanning dependencies of target APIHeaders
[ 0%] Built target APIHeaders
Scanning dependencies of target AlgorithmsHeaders
[ 0%] Built target AlgorithmsHeaders
Scanning dependencies of target BamTools
[ 1%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
[ 3%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o
[ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o
[ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o
[ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o
[ 9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o
[ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o
[ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o
[ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o
[ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o
[ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o
[ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o
[ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
[ 22%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o
[ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o
[ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o
[ 27%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o
[ 29%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o
[ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o
[ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o
[ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o
[ 37%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o
[ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o
[ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o
[ 42%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o
[ 44%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o
[ 45%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o
[ 47%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o
[ 49%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o
[ 50%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o
[ 52%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o
[ 54%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o
[ 55%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
[ 57%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
[ 59%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
[ 60%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
[ 62%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
[ 63%] Linking CXX static library libbamtools.a
[ 63%] Built target BamTools
Scanning dependencies of target jsoncpp
[ 65%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/jsoncpp.cpp.o
[ 67%] Linking CXX static library libjsoncpp.a
[ 67%] Built target jsoncpp
Scanning dependencies of target BamTools-utils
[ 68%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
[ 70%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
[ 72%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
[ 73%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
[ 75%] Linking CXX static library libbamtools-utils.a
[ 75%] Built target BamTools-utils
Scanning dependencies of target bamtools_cmd
[ 77%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
[ 78%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
[ 80%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
[ 81%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o
[ 83%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o
[ 85%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o
[ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o
[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o
[ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
[ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o
[ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o
[ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o
[ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o
[ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o
[100%] Linking CXX executable bamtools
[100%] Built target bamtools_cmd
rm -rf htslib/
git clone --recursive https://github.com/samtools/htslib.git
Cloning into 'htslib'...
remote: Enumerating objects: 10, done.
remote: Counting objects: 100% (10/10), done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 11614 (delta 1), reused 3 (delta 0), pack-reused 11604
Receiving objects: 100% (11614/11614), 8.50 MiB | 6.15 MiB/s, done.
Resolving deltas: 100% (8214/8214), done.
cd htslib/ && make && cd ../
echo '/* Default config.h generated by Makefile /' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
echo '#define HAVE_LIBCURL 1' >> config.h
gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c
gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I. -c -o header.o header.c
gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9-288-g830c061"' > version.h
gcc -g -Wall -O2 -I. -c -o hts.o hts.c
gcc -g -Wall -O2 -I. -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -I. -c -o md5.o md5.c
gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c
gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c
gcc -g -Wall -O2 -I. -c -o realn.o realn.c
gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I. -c -o region.o region.c
gcc -g -Wall -O2 -I. -c -o sam.o sam.c
gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c
gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -I. -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o
ranlib libhts.a
gcc -dynamiclib -install_name /usr/local/lib/libhts.2to3part10.dylib -current_version 1.9.255 -compatibility_version 2.10 -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o -lz -lm -lbz2 -llzma -lcurl
ln -sf libhts.dylib libhts.2to3part10.dylib
gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c
gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c
gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c
gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/hts_endian.o test/hts_endian.c
gcc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma -lcurl
gcc -g -Wall -O2 -I. -c -o test/fieldarith.o test/fieldarith.c
gcc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/hfile.o test/hfile.c
gcc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/pileup.o test/pileup.c
gcc -o test/pileup test/pileup.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/sam.o test/sam.c
gcc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c
gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_kstring.o test/test_kstring.c
gcc -o test/test_kstring test/test_kstring.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_realn.o test/test_realn.c
gcc -o test/test_realn test/test_realn.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c
gcc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c
gcc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_index.o test/test_index.c
gcc -o test/test_index test/test_index.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -g -Wall -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -o test/test-parse-reg test/test-parse-reg.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
rm -rf libgab/
git clone --recursive https://github.com/grenaud/libgab.git
Cloning into 'libgab'...
remote: Enumerating objects: 300, done.
remote: Total 300 (delta 0), reused 0 (delta 0), pack-reused 300
Receiving objects: 100% (300/300), 114.47 KiB | 626.00 KiB/s, done.
Resolving deltas: 100% (187/187), done.
make -C libgab
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c utils.cpp -o utils.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c testUtils.cpp -o testUtils.o
testUtils.cpp: In function ‘int main(int, char*)’:
testUtils.cpp:22:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
for(unsigned int c= 2147400000;c<10147400000;c+=1000000)
^~~
testUtils.cpp:24:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
return 0;
^~~~~~
make -C gzstream/
g++ -I. -O -c -o gzstream.o gzstream.C
ar cr libgzstream.a gzstream.o
g++ -o testUtils testUtils.o utils.o gzstream/libgzstream.a -lz
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c ReconsReferenceBAM.cpp -o ReconsReferenceBAM.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c PutProgramInHeader.cpp -o PutProgramInHeader.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c FastQObj.cpp -o FastQObj.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c FastQParser.cpp -o FastQParser.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c testRecons.cpp -o testRecons.o
g++ -o testRecons testRecons.o utils.o /Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/libbamtools.a ReconsReferenceBAM.o gzstream/libgzstream.a -lz
Undefined symbols for architecture x86_64:
"BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)", referenced from:
_main in testRecons.o
"BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char*&, unsigned int const&, unsigned int&) const", referenced from:
reconstructRefWithPosOnRead[abi:cxx11](BamTools::BamAlignment const*) in ReconsReferenceBAM.o
reconstructRefWithPos[abi:cxx11](BamTools::BamAlignment const*) in ReconsReferenceBAM.o
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::at(unsigned long) const", referenced from:
BamTools::Internal::SamHeaderValidator::CheckNameFormat(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamHeaderValidator_p.cpp.o)
BamTools::Internal::SamHeaderValidator::CheckSequencingTechnology(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamHeaderValidator_p.cpp.o)
BamTools::Internal::HttpRequestHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::find(char, unsigned long) const", referenced from:
BamTools::Internal::SamHeaderValidator::ValidateVersion() in libbamtools.a(SamHeaderValidator_p.cpp.o)
BamTools::Internal::BamFtp::ParseUrl(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamFtp_p.cpp.o)
BamTools::Internal::BamFtp::ParsePassiveResponse() in libbamtools.a(BamFtp_p.cpp.o)
BamTools::Internal::BamHttp::ParseUrl(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamHttp_p.cpp.o)
BamTools::Internal::HttpHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
BamTools::Internal::HttpRequestHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
BamTools::Internal::HttpResponseHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::rfind(char, unsigned long) const", referenced from:
BamTools::Internal::BamIndexFactory::CreateIndexFromFilename(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, BamTools::Internal::BamReaderPrivate*) in libbamtools.a(BamIndexFactory_p.cpp.o)
BamTools::Internal::BamIndexFactory::FileExtension(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamIndexFactory_p.cpp.o)
BamTools::Internal::HostAddress::ParseAddress() in libbamtools.a(HostAddress_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::compare(unsigned long, unsigned long, char const*, unsigned long) const", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamDeviceFactory::CreateDevice(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamDeviceFactory_p.cpp.o)
"std::__1::__vector_base_common::__throw_length_error() const", referenced from:
BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::BamAlignment::GetSoftClips(std::__1::vector<int, std::__1::allocator >&, std::__1::vector<int, std::__1::allocator >&, std::__1::vector<int, std::__1::allocator >&, bool) const in libbamtools.a(BamAlignment.cpp.o)
void std::__1::vector<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > > >::__push_back_slow_path<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const>(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::LoadNextAlignment(BamTools::BamAlignment&) in libbamtools.a(BamReader_p.cpp.o)
void std::__1::vector<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > > >::__push_back_slow_path<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const>(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamReader_p.cpp.o)
void std::__1::vector<BamTools::RefData, std::__1::allocatorBamTools::RefData >::__push_back_slow_path<BamTools::RefData const>(BamTools::RefData const&) in libbamtools.a(BamReader_p.cpp.o)
std::__1::vector<BamTools::CustomHeaderTag, std::__1::allocatorBamTools::CustomHeaderTag >::vector(std::__1::vector<BamTools::CustomHeaderTag, std::__1::allocatorBamTools::CustomHeaderTag > const&) in libbamtools.a(SamHeader.cpp.o)
...
"std::__1::__vector_base_common::__throw_out_of_range() const", referenced from:
BamTools::SamProgramChain::operator[](std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamProgramChain.cpp.o)
BamTools::SamSequenceDictionary::Remove(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamSequenceDictionary.cpp.o)
BamTools::SamSequenceDictionary::operator[](std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamSequenceDictionary.cpp.o)
BamTools::SamReadGroupDictionary::Remove(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamReadGroupDictionary.cpp.o)
BamTools::SamReadGroupDictionary::operator[](std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamReadGroupDictionary.cpp.o)
BamTools::Internal::BamToolsIndex::ReadReferenceEntry(BamTools::Internal::BtiReferenceEntry&) in libbamtools.a(BamToolsIndex_p.cpp.o)
BamTools::Internal::BamToolsIndex::HasAlignments(int const&) const in libbamtools.a(BamToolsIndex_p.cpp.o)
...
"std::__1::__basic_string_common::__throw_length_error() const", referenced from:
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, char) in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::Close() in libbamtools.a(BamReader_p.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::GetNextAlignmentCore(BamTools::BamAlignment&) in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::LoadReferenceData() in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::Open(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamReader_p.cpp.o)
...
"std::__1::locale::use_facet(std::__1::locale::id&) const", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BamRandomAccessController_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >::operator<<(std::__1::basic_ostream<char, std::__1::char_traits >& ()(std::__1::basic_ostream<char, std::__1::char_traits >&)) in libbamtools.a(SamProgramChain.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const, unsigned long) in libbamtools.a(SamProgramChain.cpp.o)
BamTools::Internal::SamFormatParser::Parse(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::BamStandardIndex::Create() in libbamtools.a(BamStandardIndex_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::ios_base::getloc() const", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BamRandomAccessController_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >::operator<<(std::__1::basic_ostream<char, std::__1::char_traits >& ()(std::__1::basic_ostream<char, std::__1::char_traits >&)) in libbamtools.a(SamProgramChain.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const, unsigned long) in libbamtools.a(SamProgramChain.cpp.o)
BamTools::Internal::SamFormatParser::Parse(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::BamStandardIndex::Create() in libbamtools.a(BamStandardIndex_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::at(unsigned long)", referenced from:
BamTools::Internal::HttpResponseHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::append(char const*, unsigned long)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::Tag2Cigar(BamTools::BamAlignment&, BamTools::RaiiBuffer&) in libbamtools.a(BamReader_p.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, char const*) in libbamtools.a(BamReader_p.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamRandomAccessController_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::append(unsigned long, char)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::assign(char const*)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
BamTools::SamHeader::SetHeaderText(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamHeader.cpp.o)
BamTools::Internal::BamToolsIndex::Create() in libbamtools.a(BamToolsIndex_p.cpp.o)
BamTools::Internal::BamToolsIndex::Jump(BamTools::BamRegion const&, bool*) in libbamtools.a(BamToolsIndex_p.cpp.o)
BamTools::Internal::BamToolsIndex::Load(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamToolsIndex_p.cpp.o)
BamTools::Internal::BamStandardIndex::Create() in libbamtools.a(BamStandardIndex_p.cpp.o)
BamTools::Internal::BamStandardIndex::Jump(BamTools::BamRegion const&, bool*) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::assign(char const*, unsigned long)", referenced from:
BamTools::BamAlignment::RemoveTag(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::LoadNextAlignment(BamTools::BamAlignment&) in libbamtools.a(BamReader_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::resize(unsigned long, char)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BamRandomAccessController_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(SamHeader.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(SamFormatParser_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::str(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::reserve(unsigned long)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::Tag2Cigar(BamTools::BamAlignment&, BamTools::RaiiBuffer&) in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamHttp::ParseUrl(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamHttp_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::push_back(char)", referenced from:
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, char) in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BamRandomAccessController_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(SamHeader.cpp.o)
std::__1::basic_istream<char, std::__1::char_traits >& std::__1::getline<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_istream<char, std::__1::char_traits >&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >&, char) in libbamtools.a(SamFormatParser_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(SamFormatParser_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::basic_string(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&)", referenced from:
BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::BamAlignment::GetErrorString() const in libbamtools.a(BamAlignment.cpp.o)
BamTools::BamAlignment::GetTagNames() const in libbamtools.a(BamAlignment.cpp.o)
void std::__1::vector<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > > >::__push_back_slow_path<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const>(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::Filename() const in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::GetErrorString() const in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::GetReferenceID(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) const in libbamtools.a(BamReader_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::basic_string(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, unsigned long, unsigned long, std::__1::allocator const&)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamIndexFactory::CreateIndexFromFilename(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, BamTools::Internal::BamReaderPrivate*) in libbamtools.a(BamIndexFactory_p.cpp.o)
BamTools::Internal::BamIndexFactory::FileExtension(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamIndexFactory_p.cpp.o)
BamTools::Internal::SamFormatParser::ParseSamLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::SamFormatParser::ParseHDLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::SamFormatParser::ParseSQLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::SamFormatParser::ParseRGLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::~basic_string()", referenced from:
BamTools::BamAlignment::SetErrorString(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) const in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::SetErrorString(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator

Answer 1 · 2019-08-14T09:26:53.000Z

I just removed bamtools from the program. There are now 1 class from bamtools that I have included with the package but it removes any cmake problems/dependency. I just built it on my colleague's Mac laptop. Could you try to give it a go now?