Wham installation fails
cccnrc opened this issue · comments
I tried to install Whamg on Ubuntu 18.04, I have installed OpenMP and CMake, but when I run
git clone --recursive https://github.com/zeeev/wham.git; cd wham; make
I got:
enrico@godzilla:/media/mothra/enrico/whamg$ git clone --recursive https://github.com/zeeev/wham.git; cd wham; make
Cloning into 'wham'...
remote: Enumerating objects: 2958, done.
remote: Total 2958 (delta 0), reused 0 (delta 0), pack-reused 2958
Receiving objects: 100% (2958/2958), 95.44 MiB | 11.17 MiB/s, done.
Resolving deltas: 100% (1922/1922), done.
Submodule 'src/Complete-Striped-Smith-Waterman-Library' (https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.git) registered for path 'src/Complete-Striped-Smith-Waterman-Library'
Submodule 'src/bamtools' (https://github.com/pezmaster31/bamtools.git) registered for path 'src/bamtools'
Submodule 'src/fastahack' (https://github.com/ekg/fastahack.git) registered for path 'src/fastahack'
Submodule 'src/seqan' (https://github.com/seqan/seqan.git) registered for path 'src/seqan'
Cloning into '/media/mothra/enrico/whamg/wham/src/Complete-Striped-Smith-Waterman-Library'...
remote: Enumerating objects: 9, done.
remote: Counting objects: 100% (9/9), done.
remote: Compressing objects: 100% (7/7), done.
remote: Total 1579 (delta 2), reused 8 (delta 2), pack-reused 1570
Receiving objects: 100% (1579/1579), 12.18 MiB | 11.11 MiB/s, done.
Resolving deltas: 100% (980/980), done.
Cloning into '/media/mothra/enrico/whamg/wham/src/bamtools'...
remote: Enumerating objects: 291, done.
remote: Counting objects: 100% (291/291), done.
remote: Compressing objects: 100% (193/193), done.
remote: Total 5148 (delta 176), reused 160 (delta 94), pack-reused 4857
Receiving objects: 100% (5148/5148), 6.28 MiB | 10.84 MiB/s, done.
Resolving deltas: 100% (3549/3549), done.
Cloning into '/media/mothra/enrico/whamg/wham/src/fastahack'...
remote: Enumerating objects: 227, done.
remote: Total 227 (delta 0), reused 0 (delta 0), pack-reused 227
Receiving objects: 100% (227/227), 51.19 KiB | 6.40 MiB/s, done.
Resolving deltas: 100% (128/128), done.
Cloning into '/media/mothra/enrico/whamg/wham/src/seqan'...
remote: Enumerating objects: 82092, done.
remote: Total 82092 (delta 0), reused 0 (delta 0), pack-reused 82092
Receiving objects: 100% (82092/82092), 148.96 MiB | 11.06 MiB/s, done.
Resolving deltas: 100% (60918/60918), done.
Submodule path 'src/Complete-Striped-Smith-Waterman-Library': checked out '8c9933a1685e0ab50c7d8b7926c9068bc0c9d7d2'
Submodule path 'src/bamtools': checked out '2d7685d2aeedd11c46ad3bd67886d9ed65c30f3e'
Submodule path 'src/fastahack': checked out '0a8ca3de9239b061839418b306bb6a9072990158'
Submodule path 'src/seqan': checked out '7f3ca44fbe777f3b637ff57ccc1dcd975cca1661'
mkdir bin
cd src/bamtools && mkdir -p build && cd build && cmake .. && make
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /media/mothra/enrico/whamg/wham/src/bamtools/build
make[1]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[2]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target SharedHeaders
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 0%] Built target SharedHeaders
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target BamTools-static
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 1%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o
[ 2%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o
[ 3%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o
[ 4%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o
[ 5%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o
[ 6%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o
[ 7%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o
[ 8%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
[ 9%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
[ 10%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
[ 11%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o
[ 12%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o
[ 12%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o
[ 13%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o
[ 14%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o
[ 15%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o
[ 16%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o
[ 17%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 18%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o
[ 19%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 20%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o
[ 21%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o
[ 22%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
[ 23%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o
[ 24%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o
[ 25%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o
[ 26%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
~~~~~~~~~~~~~^~~~~~~~~~~~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if ( i != 0 )
^~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) |
^~
[ 27%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o
[ 28%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o
[ 29%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o
[ 30%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o
[ 31%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o
[ 32%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o
[ 33%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
[ 34%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o
[ 35%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o
[ 36%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o
[ 37%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
[ 38%] Linking CXX static library ../../../lib/libbamtools.a
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 38%] Built target BamTools-static
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target BamTools
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
[ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o
[ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o
[ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o
[ 42%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o
[ 43%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o
[ 44%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o
[ 45%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o
[ 46%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o
[ 47%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o
[ 48%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o
[ 49%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o
[ 50%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
[ 51%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o
[ 52%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o
[ 53%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o
[ 54%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o
[ 55%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 56%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o
[ 57%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 58%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o
[ 59%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o
[ 60%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
[ 61%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o
[ 62%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o
[ 63%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o
[ 64%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
~~~~~~~~~~~~~^~~~~~~~~~~~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if ( i != 0 )
^~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) |
^~
[ 65%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o
[ 66%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o
[ 67%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o
[ 68%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o
[ 69%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o
[ 70%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o
[ 71%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
[ 72%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
[ 73%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
[ 74%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
[ 75%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
[ 76%] Linking CXX shared library ../../../lib/libbamtools.so
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 76%] Built target BamTools
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target APIHeaders
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 76%] Built target APIHeaders
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target AlgorithmsHeaders
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 76%] Built target AlgorithmsHeaders
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target jsoncpp
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 77%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o
[ 78%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o
[ 79%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o
[ 80%] Linking CXX static library ../../../../lib/libjsoncpp.a
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 80%] Built target jsoncpp
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target BamTools-utils
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 81%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
[ 82%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
[ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
[ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
[ 85%] Linking CXX static library ../../../lib/libbamtools-utils.a
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 85%] Built target BamTools-utils
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target bamtools_cmd
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
[ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
[ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o
[ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o
[ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o
[ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o
[ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o
[ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::ReadNamesFileReader::Read(std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:415:74: error: no matching function for call to ‘make_pair<std::__cxx11::string, bool>(__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > >::value_type&, bool)’
resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ;
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
make_pair(_T1&& __x, _T2&& __y)
^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note: template argument deduction/substitution failed:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:415:74: note: cannot convert ‘fields.std::vector<std::__cxx11::basic_string<char> >::operator[](1)’ (type ‘__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > >::value_type {aka std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’
resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ;
^
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::StatsFileReader::ParseReadGroupLine(const string&, std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:612:75: error: no matching function for call to ‘make_pair<std::__cxx11::string, ReadGroupResolver>(const string&, ReadGroupResolver&)’
readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) );
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
make_pair(_T1&& __x, _T2&& __y)
^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note: template argument deduction/substitution failed:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:612:61: note: cannot convert ‘name’ (type ‘const string {aka const std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’
readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) );
^~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::ResolveToolPrivate::MakeStats()’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1019:93: error: no matching function for call to ‘make_pair<std::__cxx11::string, bool>(std::__cxx11::string&, const bool&)’
else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) );
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
make_pair(_T1&& __x, _T2&& __y)
^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note: template argument deduction/substitution failed:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1019:68: note: cannot convert ‘al.BamTools::BamAlignment::Name’ (type ‘std::__cxx11::string {aka std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’
else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) );
~~~^~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘void BamTools::ResolveTool::ResolveToolPrivate::ParseHeader(const BamTools::SamHeader&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1051:93: error: no matching function for call to ‘make_pair<std::__cxx11::string, ReadGroupResolver>(const string&, ReadGroupResolver)’
m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) );
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,
from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
make_pair(_T1&& __x, _T2&& __y)
^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note: template argument deduction/substitution failed:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1051:70: note: cannot convert ‘rg.BamTools::SamReadGroup::ID’ (type ‘const string {aka const std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’
m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) );
~~~^~
src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make:254: recipe for target 'src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o' failed
make[3]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o] Error 1
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
CMakeFiles/Makefile2:520: recipe for target 'src/toolkit/CMakeFiles/bamtools_cmd.dir/all' failed
make[2]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/all] Error 2
make[2]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Makefile:129: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Makefile:26: recipe for target 'src/bamtools/lib/libbamtools.a' failed
make: *** [src/bamtools/lib/libbamtools.a] Error 2
Thank you in advance for any help!
I was in the same situation. I tried sudo make and installed it successfully.
still not working:
git clone --recursive https://github.com/zeeev/wham.git; cd wham; sudo make; Cloning into 'wham'... remote: Enumerating objects: 2958, done. remote: Total 2958 (delta 0), reused 0 (delta 0), pack-reused 2958 Receiving objects: 100% (2958/2958), 95.44 MiB | 11.16 MiB/s, done. Resolving deltas: 100% (1922/1922), done. Submodule 'src/Complete-Striped-Smith-Waterman-Library' (https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.git) registered for path 'src/Complete-Striped-Smith-Waterman-Library' Submodule 'src/bamtools' (https://github.com/pezmaster31/bamtools.git) registered for path 'src/bamtools' Submodule 'src/fastahack' (https://github.com/ekg/fastahack.git) registered for path 'src/fastahack' Submodule 'src/seqan' (https://github.com/seqan/seqan.git) registered for path 'src/seqan' Cloning into '/media/mothra/enrico/whamg/wham/src/Complete-Striped-Smith-Waterman-Library'... remote: Enumerating objects: 9, done. remote: Counting objects: 100% (9/9), done. remote: Compressing objects: 100% (7/7), done. remote: Total 1579 (delta 2), reused 8 (delta 2), pack-reused 1570 Receiving objects: 100% (1579/1579), 12.18 MiB | 11.02 MiB/s, done. Resolving deltas: 100% (980/980), done. Cloning into '/media/mothra/enrico/whamg/wham/src/bamtools'... remote: Enumerating objects: 291, done. remote: Counting objects: 100% (291/291), done. remote: Compressing objects: 100% (193/193), done. remote: Total 5148 (delta 176), reused 160 (delta 94), pack-reused 4857 Receiving objects: 100% (5148/5148), 6.28 MiB | 10.47 MiB/s, done. Resolving deltas: 100% (3549/3549), done. Cloning into '/media/mothra/enrico/whamg/wham/src/fastahack'... remote: Enumerating objects: 227, done. remote: Total 227 (delta 0), reused 0 (delta 0), pack-reused 227 Receiving objects: 100% (227/227), 51.19 KiB | 4.65 MiB/s, done. Resolving deltas: 100% (128/128), done. Cloning into '/media/mothra/enrico/whamg/wham/src/seqan'... remote: Enumerating objects: 82092, done. remote: Total 82092 (delta 0), reused 0 (delta 0), pack-reused 82092 Receiving objects: 100% (82092/82092), 148.96 MiB | 11.03 MiB/s, done. Resolving deltas: 100% (60918/60918), done. Submodule path 'src/Complete-Striped-Smith-Waterman-Library': checked out '8c9933a1685e0ab50c7d8b7926c9068bc0c9d7d2' Submodule path 'src/bamtools': checked out '2d7685d2aeedd11c46ad3bd67886d9ed65c30f3e' Submodule path 'src/fastahack': checked out '0a8ca3de9239b061839418b306bb6a9072990158' Submodule path 'src/seqan': checked out '7f3ca44fbe777f3b637ff57ccc1dcd975cca1661' [sudo] password for enrico: mkdir bin cd src/bamtools && mkdir -p build && cd build && cmake .. && make -- The C compiler identification is GNU 7.5.0 -- The CXX compiler identification is GNU 7.5.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /media/mothra/enrico/whamg/wham/src/bamtools/build make[1]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[2]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target SharedHeaders make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 0%] Built target SharedHeaders make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target BamTools-static make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 1%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o [ 2%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o [ 3%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o [ 4%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o [ 5%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o [ 6%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o [ 7%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o [ 8%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o [ 9%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o [ 10%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o [ 11%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o [ 12%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o [ 12%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o [ 13%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 14%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o [ 15%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o [ 16%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o [ 17%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) ) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o [ 19%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o [ 20%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o [ 21%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o [ 22%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ [ 23%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o [ 24%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o [ 25%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o [ 26%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] return m_ip4Address < m_ip4Address; ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if ( i != 0 ) ^~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | ^~ [ 27%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o [ 28%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o [ 29%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o [ 30%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o [ 31%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o [ 32%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o [ 33%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o [ 34%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o [ 35%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o [ 36%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o [ 37%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o [ 38%] Linking CXX static library ../../../lib/libbamtools.a make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 38%] Built target BamTools-static make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target BamTools make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o [ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o [ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o [ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o [ 42%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o [ 43%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o [ 44%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o [ 45%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o [ 46%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o [ 47%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o [ 48%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o [ 49%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o [ 50%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o [ 51%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 52%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o [ 53%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o [ 54%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o [ 55%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) ) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o [ 57%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o [ 58%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o [ 59%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o [ 60%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ [ 61%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o [ 62%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o [ 63%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o [ 64%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] return m_ip4Address < m_ip4Address; ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if ( i != 0 ) ^~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | ^~ [ 65%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o [ 66%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o [ 67%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o [ 68%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o [ 69%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o [ 70%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o [ 71%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o [ 72%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o [ 73%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o [ 74%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o [ 75%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o [ 76%] Linking CXX shared library ../../../lib/libbamtools.so make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 76%] Built target BamTools make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target APIHeaders make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 76%] Built target APIHeaders make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target AlgorithmsHeaders make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 76%] Built target AlgorithmsHeaders make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target jsoncpp make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 77%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o [ 78%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o [ 79%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o [ 80%] Linking CXX static library ../../../../lib/libjsoncpp.a make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 80%] Built target jsoncpp make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target BamTools-utils make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 81%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o [ 82%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o [ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o [ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o [ 85%] Linking CXX static library ../../../lib/libbamtools-utils.a make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 85%] Built target BamTools-utils make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target bamtools_cmd make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o [ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o [ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o [ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o [ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o [ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o [ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o [ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::ReadNamesFileReader::Read(std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:415:74: error: no matching function for call to ‘make_pair<std::__cxx11::string, bool>(__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > >::value_type&, bool)’ resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ; ^ In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0, from /usr/include/c++/7/bits/char_traits.h:39, from /usr/include/c++/7/string:40, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10: /usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) make_pair(_T1&& __x, _T2&& __y) ^~~~~~~~~ /usr/include/c++/7/bits/stl_pair.h:524:5: note: template argument deduction/substitution failed: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:415:74: note: cannot convert ‘fields.std::vector<std::__cxx11::basic_string<char> >::operator[](1)’ (type ‘__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > >::value_type {aka std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’ resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ; ^ /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::StatsFileReader::ParseReadGroupLine(const string&, std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:612:75: error: no matching function for call to ‘make_pair<std::__cxx11::string, ReadGroupResolver>(const string&, ReadGroupResolver&)’ readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) ); ^ In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0, from /usr/include/c++/7/bits/char_traits.h:39, from /usr/include/c++/7/string:40, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10: /usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) make_pair(_T1&& __x, _T2&& __y) ^~~~~~~~~ /usr/include/c++/7/bits/stl_pair.h:524:5: note: template argument deduction/substitution failed: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:612:61: note: cannot convert ‘name’ (type ‘const string {aka const std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’ readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) ); ^~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::ResolveToolPrivate::MakeStats()’: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1019:93: error: no matching function for call to ‘make_pair<std::__cxx11::string, bool>(std::__cxx11::string&, const bool&)’ else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) ); ^ In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0, from /usr/include/c++/7/bits/char_traits.h:39, from /usr/include/c++/7/string:40, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10: /usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) make_pair(_T1&& __x, _T2&& __y) ^~~~~~~~~ /usr/include/c++/7/bits/stl_pair.h:524:5: note: template argument deduction/substitution failed: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1019:68: note: cannot convert ‘al.BamTools::BamAlignment::Name’ (type ‘std::__cxx11::string {aka std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’ else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) ); ~~~^~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘void BamTools::ResolveTool::ResolveToolPrivate::ParseHeader(const BamTools::SamHeader&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1051:93: error: no matching function for call to ‘make_pair<std::__cxx11::string, ReadGroupResolver>(const string&, ReadGroupResolver)’ m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) ); ^ In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0, from /usr/include/c++/7/bits/char_traits.h:39, from /usr/include/c++/7/string:40, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13, from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10: /usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) make_pair(_T1&& __x, _T2&& __y) ^~~~~~~~~ /usr/include/c++/7/bits/stl_pair.h:524:5: note: template argument deduction/substitution failed: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1051:70: note: cannot convert ‘rg.BamTools::SamReadGroup::ID’ (type ‘const string {aka const std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’ m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) ); ~~~^~ src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make:254: recipe for target 'src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o' failed make[3]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o] Error 1 make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' CMakeFiles/Makefile2:520: recipe for target 'src/toolkit/CMakeFiles/bamtools_cmd.dir/all' failed make[2]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/all] Error 2 make[2]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Makefile:129: recipe for target 'all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Makefile:26: recipe for target 'src/bamtools/lib/libbamtools.a' failed make: *** [src/bamtools/lib/libbamtools.a] Error 2