* Package: sci-biology/bamtools-2.3.0
* Repository: gentoo
* Maintainer: mmokrejs@gmail.com sci-biology@gentoo.org,proxy-maint@gentoo.org
* USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
* FEATURES: preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking bamtools-2.3.0.tar.gz to /var/tmp/portage/sci-biology/bamtools-2.3.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/bamtools-2.3.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0 ...
* Applying bamtools-2.3.0-unbundle.patch ...
[ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build"
cmake --no-warn-unused-cli -C /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/gentoo_toolchain.cmake /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0
Not searching for unused variables given on the command line.
loading initial cache file /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 6.2.0
-- The CXX compiler identification is GNU 6.2.0
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
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-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- <<< Gentoo configuration >>>
Build type Gentoo
Install path /usr
Compiler flags:
C -march=native -O2 -pipe
C++ -march=native -O2 -pipe
Linker flags:
Executable -Wl,-O1 -Wl,--as-needed
Module -Wl,-O1 -Wl,--as-needed
Shared -Wl,-O1 -Wl,--as-needed
-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build"
make -j1 VERBOSE=1
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make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
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cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0 /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/CMakeFiles/SharedHeaders.dir/DependInfo.cmake
Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/CMakeFiles/SharedHeaders.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/CMakeFiles/SharedHeaders.dir/depend.internal".
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cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamWriter.cpp
[ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamHeader.cpp
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[ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamProgramChain.cpp
[ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o
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[ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o
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[ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o
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[ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
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[ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o
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/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp: In member function 'void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/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)) )
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/index/BamToolsIndex_p.cpp
[ 20%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamDeviceFactory_p.cpp
[ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamFile_p.cpp
[ 22%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamFtp_p.cpp
[ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendGetRequest(size_t)':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/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 ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendHeadRequest()':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/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 ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
[ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamPipe_p.cpp
[ 25%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BgzfStream_p.cpp
[ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/ByteArray_p.cpp
[ 27%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp: In member function 'bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
~~~~~~~~~~~~~^~~~~~~~~~~~~~
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp: In member function 'std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ( i != 0 )
^~
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) |
^~
[ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostInfo_p.cpp
[ 29%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HttpHeader_p.cpp
[ 30%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/ILocalIODevice_p.cpp
[ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/RollingBuffer_p.cpp
[ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.cpp
[ 33%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_p.cpp
[ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_unix_p.cpp
[ 35%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.cpp
[ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.cpp
[ 37%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.cpp
[ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/utils/BamException_p.cpp
[ 39%] Linking CXX shared library /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.so
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1
/usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libbamtools.so.2.3.0 -o /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.so.2.3.0 CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -lz
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E cmake_symlink_library /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.so.2.3.0 /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.so.2.3.0 /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.so
make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
[ 39%] Built target BamTools
make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/depend
make[2]: Entering directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0 /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/AlgorithmsHeaders.dir/DependInfo.cmake
Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/AlgorithmsHeaders.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/AlgorithmsHeaders.dir/depend.internal".
Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/AlgorithmsHeaders.dir/depend.internal".
Scanning dependencies of target AlgorithmsHeaders
make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/build
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Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/BamTools-static.dir/depend.internal".
Scanning dependencies of target BamTools-static
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[ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o
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[ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
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[ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
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[ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
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[ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o
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[ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o
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[ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o
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[ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o
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[ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o
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[ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp: In member function 'void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/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)) )
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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[ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamFile_p.cpp
[ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamFtp_p.cpp
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cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendGetRequest(size_t)':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/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 ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendHeadRequest()':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/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 ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
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cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BamPipe_p.cpp
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cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/BgzfStream_p.cpp
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cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/ByteArray_p.cpp
[ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp: In member function 'bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
~~~~~~~~~~~~~^~~~~~~~~~~~~~
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp: In member function 'std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ( i != 0 )
^~
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) |
^~
[ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HostInfo_p.cpp
[ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/HttpHeader_p.cpp
[ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/ILocalIODevice_p.cpp
[ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/RollingBuffer_p.cpp
[ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.cpp
[ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_p.cpp
[ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_unix_p.cpp
[ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.cpp
[ 76%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.cpp
[ 77%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.cpp
[ 78%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/x86_64-pc-linux-gnu-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -DNDEBUG -march=native -O2 -pipe -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/utils/BamException_p.cpp
[ 79%] Linking CXX static library /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.a
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -P CMakeFiles/BamTools-static.dir/cmake_clean_target.cmake
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools-static.dir/link.txt --verbose=1
/usr/bin/x86_64-pc-linux-gnu-ar qc /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.a CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o CMakeFiles/BamTools-static.dir/BamReader.cpp.o CMakeFiles/BamTools-static.dir/BamWriter.cpp.o CMakeFiles/BamTools-static.dir/SamHeader.cpp.o CMakeFiles/BamTools-static.dir/SamProgram.cpp.o CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools-static.dir/SamSequence.cpp.o CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
/usr/bin/x86_64-pc-linux-gnu-ranlib /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools.a
make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
[ 79%] Built target BamTools-static
make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/depend
make[2]: Entering directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0 /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/APIHeaders.dir/DependInfo.cmake
Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/APIHeaders.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/APIHeaders.dir/depend.internal".
Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/APIHeaders.dir/depend.internal".
Scanning dependencies of target APIHeaders
make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/build
make[2]: Entering directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/api_global.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/api_global.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamAlgorithms.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/BamAlgorithms.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamAlignment.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/BamAlignment.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamAux.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/BamAux.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamConstants.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/BamConstants.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamIndex.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/BamIndex.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamMultiReader.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/BamMultiReader.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamReader.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/BamReader.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamWriter.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/BamWriter.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/IBamIODevice.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/IBamIODevice.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamConstants.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/SamConstants.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamHeader.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/SamHeader.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamProgram.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/SamProgram.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamProgramChain.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/SamProgramChain.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamReadGroup.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/SamReadGroup.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamReadGroupDictionary.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/SamReadGroupDictionary.h
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamSequence.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/SamSequence.h
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cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit && /usr/bin/x86_64-pc-linux-gnu-g++ -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/utils -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/third_party -DNDEBUG -march=native -O2 -pipe -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_merge.cpp
[ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit && /usr/bin/x86_64-pc-linux-gnu-g++ -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/utils -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/third_party -DNDEBUG -march=native -O2 -pipe -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_random.cpp
[ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit && /usr/bin/x86_64-pc-linux-gnu-g++ -D_FILE_OFFSET_BITS=64 -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/utils -I/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/third_party -DNDEBUG -march=native -O2 -pipe -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp: In member function 'bool BamTools::ResolveTool::ReadNamesFileReader::Read(std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:415:74: error: no matching function for call to 'make_pair(__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/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_algobase.h:64:0,
from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/char_traits.h:39,
from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/string:40,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_tool.h:14,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.h:13,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:10:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: 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/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: note: template argument deduction/substitution failed:
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:415:74: note: cannot convert 'fields.std::vector<_Tp, _Alloc>::operator[]<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >(1ul)' (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) ) ;
^
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp: In member function 'bool BamTools::ResolveTool::StatsFileReader::ParseReadGroupLine(const string&, std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:612:75: error: no matching function for call to 'make_pair(const string&, ReadGroupResolver&)'
readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) );
^
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_algobase.h:64:0,
from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/char_traits.h:39,
from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/string:40,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_tool.h:14,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.h:13,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:10:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: 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/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: note: template argument deduction/substitution failed:
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/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) );
^~~~
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp: In member function 'bool BamTools::ResolveTool::ResolveToolPrivate::MakeStats()':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:1019:93: error: no matching function for call to 'make_pair(std::__cxx11::string&, const bool&)'
lver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) );
^
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_algobase.h:64:0,
from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/char_traits.h:39,
from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/string:40,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_tool.h:14,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.h:13,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:10:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: 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/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: note: template argument deduction/substitution failed:
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/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) );
~~~^~~~
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp: In member function 'void BamTools::ResolveTool::ResolveToolPrivate::ParseHeader(const BamTools::SamHeader&)':
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:1051:93: error: no matching function for call to 'make_pair(const string&, ReadGroupResolver)'
ups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) );
^
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_algobase.h:64:0,
from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/char_traits.h:39,
from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/string:40,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_tool.h:14,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.h:13,
from /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:10:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: 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/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: note: template argument deduction/substitution failed:
/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/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()) );
~~~^~
make[2]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make:255: src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
make[1]: *** [CMakeFiles/Makefile2:444: src/toolkit/CMakeFiles/bamtools_cmd.dir/all] Error 2
make[1]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
make: *** [Makefile:128: all] Error 2
* ERROR: sci-biology/bamtools-2.3.0::gentoo failed (compile phase):
* emake failed
*
* If you need support, post the output of `emerge --info '=sci-biology/bamtools-2.3.0::gentoo'`,
* the complete build log and the output of `emerge -pqv '=sci-biology/bamtools-2.3.0::gentoo'`.
* The complete build log is located at '/var/log/portage/sci-biology:bamtools-2.3.0:20161005-054930.log'.
* For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/bamtools-2.3.0/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sci-biology/bamtools-2.3.0/temp/environment'.
* Working directory: '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
* S: '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0'