* 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 -- Detecting C compile features - done -- 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 /usr/bin/cmake -H/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0 -B/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/CMakeFiles /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build' make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.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 /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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/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/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) + 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-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 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/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 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-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 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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 [ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.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 -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 ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ [ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.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 -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 [ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.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 -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 [ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.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 -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 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[ 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 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-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_filter.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_filter.cpp [ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.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_header.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_header.cpp [ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.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_index.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_index.cpp [ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.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_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, 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 > >::value_type&, bool)' resolver.ReadNames.insert( make_pair(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 constexpr std::pair::__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::allocator > >(1ul)' (type '__gnu_cxx::__alloc_traits > >::value_type {aka std::__cxx11::basic_string}') to type 'std::__cxx11::basic_string&&' resolver.ReadNames.insert( make_pair(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, 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(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 constexpr std::pair::__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}') to type 'std::__cxx11::basic_string&&' readGroups.insert( make_pair(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(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 constexpr std::pair::__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}') to type 'std::__cxx11::basic_string&&' else resolver.ReadNames.insert( make_pair(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(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 constexpr std::pair::__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}') to type 'std::__cxx11::basic_string&&' m_readGroups.insert( make_pair(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'