Attachment 449206 Details for Bug 596208 – sci-biology:bamtools-2.3.0:20161005-054930.log

sci-biology:bamtools-2.3.0:20161005-054930.log

sci-biology:bamtools-2.3.0:20161005-054930.log (text/plain), 93.08 KB, created by Toralf Förster on 2016-10-05 08:15:15 UTC

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Creator: Toralf Förster

Created: 2016-10-05 08:15:15 UTC

Size: 93.08 KB

patch

obsolete

> * 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".
>Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/CMakeFiles/CMakeDirectoryInformation.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".
>Scanning dependencies of target SharedHeaders
>make[2]: Leaving 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/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 && /usr/bin/cmake -E copy_if_different /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/shared/bamtools_global.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/shared/bamtools_global.h
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>[  0%] Built target SharedHeaders
>make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.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/BamTools.dir/DependInfo.cmake
>Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/BamTools.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/BamTools.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/BamTools.dir/depend.internal".
>Scanning dependencies of target BamTools
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/build
>make[2]: Entering directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>[  1%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.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/BamAlignment.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamAlignment.cpp
>[  2%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.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/BamMultiReader.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamMultiReader.cpp
>[  3%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.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/BamReader.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamReader.cpp
>[  4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.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/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
>[  6%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.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/SamProgram.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamProgram.cpp
>[  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
>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/SamReadGroup.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamReadGroup.cpp
>[  9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.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/SamReadGroupDictionary.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamReadGroupDictionary.cpp
>[ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.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/SamSequence.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamSequence.cpp
>[ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.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/SamSequenceDictionary.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamSequenceDictionary.cpp
>[ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_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/bam/BamHeader_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamHeader_p.cpp
>[ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_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/bam/BamMultiReader_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamMultiReader_p.cpp
>[ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_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/bam/BamRandomAccessController_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.cpp
>[ 15%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_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/bam/BamReader_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamReader_p.cpp
>[ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_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/bam/BamWriter_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.cpp
>[ 17%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_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/index/BamIndexFactory_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/index/BamIndexFactory_p.cpp
>[ 18%] Building CXX object src/api/CMakeFiles/BamTools.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 -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) + linearOffsets.size()*sizeof(uint64_t)) )
>          ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>[ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_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/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
>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/algorithms/Sort.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/algorithms/Sort.h
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>[ 39%] Built target AlgorithmsHeaders
>make -f src/api/CMakeFiles/BamTools-static.dir/build.make src/api/CMakeFiles/BamTools-static.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/BamTools-static.dir/DependInfo.cmake
>Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/api/CMakeFiles/BamTools-static.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/BamTools-static.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/BamTools-static.dir/depend.internal".
>Scanning dependencies of target BamTools-static
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>make -f src/api/CMakeFiles/BamTools-static.dir/build.make src/api/CMakeFiles/BamTools-static.dir/build
>make[2]: Entering directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>[ 40%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.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/BamAlignment.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamAlignment.cpp
>[ 41%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.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/BamMultiReader.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamMultiReader.cpp
>[ 42%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.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/BamReader.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamReader.cpp
>[ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.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/BamWriter.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/BamWriter.cpp
>[ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.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 -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/SamHeader.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamHeader.cpp
>[ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.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/SamProgram.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamProgram.cpp
>[ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.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 -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/SamProgramChain.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamProgramChain.cpp
>[ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.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/SamReadGroup.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamReadGroup.cpp
>[ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.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/SamReadGroupDictionary.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamReadGroupDictionary.cpp
>[ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.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/SamSequence.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamSequence.cpp
>[ 51%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.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/SamSequenceDictionary.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/SamSequenceDictionary.cpp
>[ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_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/bam/BamHeader_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamHeader_p.cpp
>[ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_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/bam/BamMultiReader_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamMultiReader_p.cpp
>[ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_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/bam/BamRandomAccessController_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.cpp
>[ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_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/bam/BamReader_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamReader_p.cpp
>[ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_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/bam/BamWriter_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.cpp
>[ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_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/BamIndexFactory_p.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/api/internal/index/BamIndexFactory_p.cpp
>[ 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)) )
>          ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>[ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_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/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
>[ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.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 -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/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
>[ 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
>[ 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 /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
>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/SamSequenceDictionary.h /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/include/api/SamSequenceDictionary.h
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>[ 79%] Built target APIHeaders
>make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.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/utils /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/utils /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils/CMakeFiles/BamTools-utils.dir/DependInfo.cmake
>Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils/CMakeFiles/BamTools-utils.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils/CMakeFiles/BamTools-utils.dir/depend.internal".
>Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils/CMakeFiles/BamTools-utils.dir/depend.internal".
>Scanning dependencies of target BamTools-utils
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/build
>make[2]: Entering directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>[ 80%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
>cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils && /usr/bin/x86_64-pc-linux-gnu-g++  -DBAMTOOLS_UTILS_LIBRARY -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   -DNDEBUG -march=native -O2 -pipe    -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/utils/bamtools_fasta.cpp
>[ 81%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
>cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils && /usr/bin/x86_64-pc-linux-gnu-g++  -DBAMTOOLS_UTILS_LIBRARY -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   -DNDEBUG -march=native -O2 -pipe    -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/utils/bamtools_options.cpp
>[ 82%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
>cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils && /usr/bin/x86_64-pc-linux-gnu-g++  -DBAMTOOLS_UTILS_LIBRARY -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   -DNDEBUG -march=native -O2 -pipe    -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/utils/bamtools_pileup_engine.cpp
>[ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
>cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils && /usr/bin/x86_64-pc-linux-gnu-g++  -DBAMTOOLS_UTILS_LIBRARY -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   -DNDEBUG -march=native -O2 -pipe    -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/utils/bamtools_utilities.cpp
>[ 84%] Linking CXX static library /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/lib/libbamtools-utils.a
>cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils && /usr/bin/cmake -P CMakeFiles/BamTools-utils.dir/cmake_clean_target.cmake
>cd /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools-utils.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-utils.a  CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_utilities.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-utils.a
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>[ 84%] Built target BamTools-utils
>make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.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/toolkit /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/toolkit /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake
>Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit/CMakeFiles/bamtools_cmd.dir/depend.internal".
>Dependee "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build/src/toolkit/CMakeFiles/bamtools_cmd.dir/depend.internal".
>Scanning dependencies of target bamtools_cmd
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/build
>make[2]: Entering directory '/var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0_build'
>[ 85%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.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_convert.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_convert.cpp
>[ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.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_count.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_count.cpp
>[ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.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_coverage.cpp.o -c /var/tmp/portage/sci-biology/bamtools-2.3.0/work/bamtools-2.3.0/src/toolkit/bamtools_coverage.cpp
>[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.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_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<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'

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Attachments on bug 596208: 449202 | 449204 | 449206