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| 2014-12-04 10:01:36 +0100 | |
| cmake | |
| .. | |
| -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/freebayes/0.9.14-15 | |
| -DCMAKE_BUILD_TYPE=None | |
| -DCMAKE_FIND_FRAMEWORK=LAST | |
| -DCMAKE_VERBOSE_MAKEFILE=ON | |
| -Wno-dev | |
| -- The C compiler identification is AppleClang 6.0.0.6000054 | |
| -- The CXX compiler identification is AppleClang 6.0.0.6000054 | |
| -- Check for working C compiler: /usr/local/Library/ENV/4.3/clang | |
| -- Check for working C compiler: /usr/local/Library/ENV/4.3/clang -- works | |
| -- Detecting C compiler ABI info | |
| -- Detecting C compiler ABI info - done | |
| -- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++ | |
| -- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++ -- works | |
| -- Detecting CXX compiler ABI info | |
| -- Detecting CXX compiler ABI info - done | |
| -- Configuring done | |
| -- Generating done | |
| -- Build files have been written to: /tmp/freebayes-Xwf4aL/bamtools/build |
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| clang called with: CMakeCCompilerId.c | |
| superenv executed: clang CMakeCCompilerId.c -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| clang++ called with: CMakeCXXCompilerId.cpp | |
| superenv executed: clang++ CMakeCXXCompilerId.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| clang called with: -o CMakeFiles/cmTryCompileExec2841904303.dir/testCCompiler.c.o -c /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles/CMakeTmp/testCCompiler.c | |
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| clang called with: -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTryCompileExec2841904303.dir/testCCompiler.c.o -o cmTryCompileExec2841904303 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries | |
| superenv executed: clang -pipe -w -Os -march=native -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTryCompileExec2841904303.dir/testCCompiler.c.o -o cmTryCompileExec2841904303 -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| clang called with: -o CMakeFiles/cmTryCompileExec2634388609.dir/CMakeCCompilerABI.c.o -c /usr/local/Cellar/cmake/3.0.2/share/cmake/Modules/CMakeCCompilerABI.c | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang -pipe -w -Os -march=native -o CMakeFiles/cmTryCompileExec2634388609.dir/CMakeCCompilerABI.c.o -c /usr/local/Cellar/cmake/3.0.2/share/cmake/Modules/CMakeCCompilerABI.c -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang called with: -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTryCompileExec2634388609.dir/CMakeCCompilerABI.c.o -o cmTryCompileExec2634388609 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries | |
| superenv executed: clang -pipe -w -Os -march=native -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTryCompileExec2634388609.dir/CMakeCCompilerABI.c.o -o cmTryCompileExec2634388609 -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| clang++ called with: -o CMakeFiles/cmTryCompileExec2727959958.dir/testCXXCompiler.cxx.o -c /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -o CMakeFiles/cmTryCompileExec2727959958.dir/testCXXCompiler.cxx.o -c /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTryCompileExec2727959958.dir/testCXXCompiler.cxx.o -o cmTryCompileExec2727959958 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries | |
| superenv executed: clang++ -pipe -w -Os -march=native -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTryCompileExec2727959958.dir/testCXXCompiler.cxx.o -o cmTryCompileExec2727959958 -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| clang++ called with: -o CMakeFiles/cmTryCompileExec1472697905.dir/CMakeCXXCompilerABI.cpp.o -c /usr/local/Cellar/cmake/3.0.2/share/cmake/Modules/CMakeCXXCompilerABI.cpp | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -o CMakeFiles/cmTryCompileExec1472697905.dir/CMakeCXXCompilerABI.cpp.o -c /usr/local/Cellar/cmake/3.0.2/share/cmake/Modules/CMakeCXXCompilerABI.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTryCompileExec1472697905.dir/CMakeCXXCompilerABI.cpp.o -o cmTryCompileExec1472697905 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries | |
| superenv executed: clang++ -pipe -w -Os -march=native -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTryCompileExec1472697905.dir/CMakeCXXCompilerABI.cpp.o -o cmTryCompileExec1472697905 -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
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| 2014-12-04 10:01:39 +0100 | |
| make | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -H/tmp/freebayes-Xwf4aL/bamtools -B/tmp/freebayes-Xwf4aL/bamtools/build --check-build-system CMakeFiles/Makefile.cmake 0 | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_start /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles/progress.marks | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 all | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/depend | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/freebayes-Xwf4aL/bamtools /tmp/freebayes-Xwf4aL/bamtools/src /tmp/freebayes-Xwf4aL/bamtools/build /tmp/freebayes-Xwf4aL/bamtools/build/src /tmp/freebayes-Xwf4aL/bamtools/build/src/CMakeFiles/SharedHeaders.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target SharedHeaders | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/build | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 83 | |
| [ 1%] Exporting SharedHeaders | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/shared/bamtools_global.h /tmp/freebayes-Xwf4aL/bamtools/include/shared/bamtools_global.h | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 83 | |
| [ 1%] Built target SharedHeaders | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/depend | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/freebayes-Xwf4aL/bamtools /tmp/freebayes-Xwf4aL/bamtools/src/api /tmp/freebayes-Xwf4aL/bamtools/build /tmp/freebayes-Xwf4aL/bamtools/build/src/api /tmp/freebayes-Xwf4aL/bamtools/build/src/api/CMakeFiles/APIHeaders.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target APIHeaders | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/build | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 1 | |
| [ 2%] Exporting APIHeaders | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/api_global.h /tmp/freebayes-Xwf4aL/bamtools/include/api/api_global.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/BamAlgorithms.h /tmp/freebayes-Xwf4aL/bamtools/include/api/BamAlgorithms.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/BamAlignment.h /tmp/freebayes-Xwf4aL/bamtools/include/api/BamAlignment.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/BamAux.h /tmp/freebayes-Xwf4aL/bamtools/include/api/BamAux.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/BamConstants.h /tmp/freebayes-Xwf4aL/bamtools/include/api/BamConstants.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/BamIndex.h /tmp/freebayes-Xwf4aL/bamtools/include/api/BamIndex.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/BamMultiReader.h /tmp/freebayes-Xwf4aL/bamtools/include/api/BamMultiReader.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/BamReader.h /tmp/freebayes-Xwf4aL/bamtools/include/api/BamReader.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/BamWriter.h /tmp/freebayes-Xwf4aL/bamtools/include/api/BamWriter.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/IBamIODevice.h /tmp/freebayes-Xwf4aL/bamtools/include/api/IBamIODevice.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/SamConstants.h /tmp/freebayes-Xwf4aL/bamtools/include/api/SamConstants.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/SamHeader.h /tmp/freebayes-Xwf4aL/bamtools/include/api/SamHeader.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/SamProgram.h /tmp/freebayes-Xwf4aL/bamtools/include/api/SamProgram.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/SamProgramChain.h /tmp/freebayes-Xwf4aL/bamtools/include/api/SamProgramChain.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/SamReadGroup.h /tmp/freebayes-Xwf4aL/bamtools/include/api/SamReadGroup.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/SamReadGroupDictionary.h /tmp/freebayes-Xwf4aL/bamtools/include/api/SamReadGroupDictionary.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/SamSequence.h /tmp/freebayes-Xwf4aL/bamtools/include/api/SamSequence.h | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/SamSequenceDictionary.h /tmp/freebayes-Xwf4aL/bamtools/include/api/SamSequenceDictionary.h | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 1 | |
| [ 2%] Built target APIHeaders | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/depend | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/freebayes-Xwf4aL/bamtools /tmp/freebayes-Xwf4aL/bamtools/src/api /tmp/freebayes-Xwf4aL/bamtools/build /tmp/freebayes-Xwf4aL/bamtools/build/src/api /tmp/freebayes-Xwf4aL/bamtools/build/src/api/CMakeFiles/AlgorithmsHeaders.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target AlgorithmsHeaders | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/build | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 2 | |
| [ 3%] Exporting AlgorithmsHeaders | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E copy_if_different /tmp/freebayes-Xwf4aL/bamtools/src/api/algorithms/Sort.h /tmp/freebayes-Xwf4aL/bamtools/include/api/algorithms/Sort.h | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 2 | |
| [ 3%] Built target AlgorithmsHeaders | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/depend | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/freebayes-Xwf4aL/bamtools /tmp/freebayes-Xwf4aL/bamtools/src/api /tmp/freebayes-Xwf4aL/bamtools/build /tmp/freebayes-Xwf4aL/bamtools/build/src/api /tmp/freebayes-Xwf4aL/bamtools/build/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target BamTools | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/build | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 3 | |
| [ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamAlignment.cpp | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 4 | |
| [ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamMultiReader.cpp | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 5 | |
| [ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamReader.cpp | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 6 | |
| [ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamWriter.cpp | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/sam/SamFormatParser_p.cpp | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/utils/BamException_p.cpp | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/BamWriter.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamWriter.cpp | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamHeader.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamHeader.cpp | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamProgram.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamProgram.cpp | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamProgramChain.cpp | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/api && /usr/local/Library/ENV/4.3/clang++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamReadGroup.cpp | |
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| Linking CXX static library ../../../lib/libbamtools-utils.a | |
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| /usr/bin/ar cr ../../../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 | |
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| [ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_convert.cpp | |
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| [ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_count.cpp | |
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| [ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_coverage.cpp | |
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| [ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_filter.cpp | |
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| [ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_header.cpp | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 89 | |
| [ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_index.cpp | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 90 | |
| [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_merge.cpp | |
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| [ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_random.cpp | |
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| [ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o | |
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| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 93 | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_revert.cpp | |
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| [ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_sort.cpp | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_split.cpp | |
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| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_stats.cpp | |
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| [100%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Library/ENV/4.3/clang++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools.cpp | |
| Linking CXX executable ../../../bin/bamtools | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 | |
| /usr/local/Library/ENV/4.3/clang++ -O3 -DNDEBUG -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o ../../../bin/bamtools-2.3.0 ../../../lib/libbamtools.2.3.0.dylib ../../../lib/libbamtools-utils.a ../../../lib/libjsoncpp.a ../../../lib/libbamtools.2.3.0.dylib -lz | |
| cd /tmp/freebayes-Xwf4aL/bamtools/build/src/toolkit && /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_symlink_executable ../../../bin/bamtools-2.3.0 ../../../bin/bamtools | |
| /usr/local/Cellar/cmake/3.0.2/bin/cmake -E cmake_progress_report /tmp/freebayes-Xwf4aL/bamtools/build/CMakeFiles 84 85 86 87 88 89 90 91 92 93 94 95 96 97 | |
| [100%] Built target bamtools_cmd | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamAlignment.cpp | |
| superenv removed: -O3 -Wall | |
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| superenv executed: clang++ -pipe -w -Os -march=native -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -fPIC -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamAlignment.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamMultiReader.cpp | |
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| superenv executed: clang++ -pipe -w -Os -march=native -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -fPIC -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamMultiReader.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamReader.cpp | |
| superenv removed: -O3 -Wall | |
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| superenv executed: clang++ -pipe -w -Os -march=native -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -fPIC -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamReader.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamWriter.cpp | |
| superenv removed: -O3 -Wall | |
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| superenv executed: clang++ -pipe -w -Os -march=native -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -fPIC -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/BamWriter.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamHeader.cpp | |
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| superenv executed: clang++ -pipe -w -Os -march=native -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -fPIC -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamHeader.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamProgram.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamReadGroup.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamReadGroupDictionary.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamSequence.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/SamSequenceDictionary.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/bam/BamHeader_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/bam/BamMultiReader_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/bam/BamReader_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/bam/BamWriter_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/index/BamIndexFactory_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/index/BamStandardIndex_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/index/BamToolsIndex_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/io/BamFile_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/io/BamHttp_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/sam/SamFormatParser_p.cpp | |
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| clang++ called with: -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -I/tmp/freebayes-Xwf4aL/bamtools/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_convert.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_count.cpp | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_count.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_coverage.cpp | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_coverage.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_filter.cpp | |
| superenv removed: -O3 -Wall | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_filter.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_header.cpp | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_header.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_index.cpp | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_index.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_merge.cpp | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_merge.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_random.cpp | |
| superenv removed: -O3 -Wall | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_random.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_resolve.cpp | |
| superenv removed: -O3 -Wall | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_resolve.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_revert.cpp | |
| superenv removed: -O3 -Wall | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_revert.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_sort.cpp | |
| superenv removed: -O3 -Wall | |
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| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_sort.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_split.cpp | |
| superenv removed: -O3 -Wall | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_split.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_stats.cpp | |
| superenv removed: -O3 -Wall | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools_stats.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools.cpp | |
| superenv removed: -O3 -Wall | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -D_FILE_OFFSET_BITS=64 -DNDEBUG -I/tmp/freebayes-Xwf4aL/bamtools/src -I/tmp/freebayes-Xwf4aL/bamtools/src/api -I/tmp/freebayes-Xwf4aL/bamtools/src/utils -I/tmp/freebayes-Xwf4aL/bamtools/src/third_party -o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -c /tmp/freebayes-Xwf4aL/bamtools/src/toolkit/bamtools.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| clang++ called with: -O3 -DNDEBUG -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o ../../../bin/bamtools-2.3.0 ../../../lib/libbamtools.2.3.0.dylib ../../../lib/libbamtools-utils.a ../../../lib/libjsoncpp.a ../../../lib/libbamtools.2.3.0.dylib -lz | |
| superenv removed: -O3 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries | |
| superenv executed: clang++ -pipe -w -Os -march=native -DNDEBUG -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o ../../../bin/bamtools-2.3.0 ../../../lib/libbamtools.2.3.0.dylib ../../../lib/libbamtools-utils.a ../../../lib/libjsoncpp.a ../../../lib/libbamtools.2.3.0.dylib -lz -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
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| 2014-12-04 10:02:49 +0100 | |
| make | |
| g++ -w -O3 -pipe -fomit-frame-pointer -ffast-math fsom.c split.cpp main.cpp -o fsom -lm |
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| g++ called with: -w -O3 -pipe -fomit-frame-pointer -ffast-math fsom.c split.cpp main.cpp -o fsom -lm | |
| superenv removed: -O3 | |
| superenv added: -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| superenv executed: clang++ -pipe -w -Os -march=native -w -pipe -fomit-frame-pointer -ffast-math fsom.c split.cpp main.cpp -o fsom -lm -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
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| 2014-12-04 10:02:50 +0100 | |
| make | |
| cd tabixpp && /Applications/Xcode.app/Contents/Developer/usr/bin/make | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o | |
| ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o | |
| ranlib libtabix.a | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o | |
| gcc -g -Wall -O2 -fPIC -o tabix main.o -lm -L. -ltabix -lz | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzip.c -o bgzip.o | |
| gcc -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz | |
| g++ -g -Wall -O2 -fPIC -c tabix.cpp | |
| g++ -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o bgzf.o -lm -L. -ltabix -lz | |
| g++ -c -o src/Variant.o src/Variant.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -O3 -D_FILE_OFFSET_BITS=64 | |
| g++ -c -o src/split.o src/split.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -O3 -D_FILE_OFFSET_BITS=64 | |
| cd smithwaterman && /Applications/Xcode.app/Contents/Developer/usr/bin/make | |
| g++ -c -o smithwaterman.o smithwaterman.cpp | |
| g++ -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp | |
| g++ -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp | |
| g++ -c -o Repeats.o Repeats.cpp | |
| g++ -c -o LeftAlign.o LeftAlign.cpp | |
| g++ -c -o IndelAllele.o IndelAllele.cpp | |
| g++ -c -o disorder.o disorder.c | |
| * linking smithwaterman | |
| ld: internal error: atom not found in symbolIndex(__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE6assignINS_16reverse_iteratorINS_11__wrap_iterIPcEEEEEENS_9enable_ifIXsr21__is_forward_iteratorIT_EE5valueERS5_E4typeESD_SD_) for architecture x86_64 | |
| clang: error: linker command failed with exit code 1 (use -v to see invocation) | |
| make[1]: *** [smithwaterman] Error 1 | |
| make: *** [smithwaterman/SmithWatermanGotoh.o] Error 2 | |
| HOMEBREW_VERSION: 0.9.5 | |
| HEAD: f6b84fbba9c441f13f4e6c2ee23e42ac5a9e38f9 | |
| CPU: quad-core 64-bit sandybridge | |
| OS X: 10.10.1-x86_64 | |
| Xcode: 6.1 | |
| CLT: 6.1.1.0.1.1416017670 | |
| X11: 2.7.7 => /opt/X11 |
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| gcc called with: -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang -pipe -w -Os -march=native -c -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| gcc called with: -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang -pipe -w -Os -march=native -c -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| gcc called with: -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang -pipe -w -Os -march=native -c -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| gcc called with: -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang -pipe -w -Os -march=native -c -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| gcc called with: -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang -pipe -w -Os -march=native -c -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| gcc called with: -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang -pipe -w -Os -march=native -c -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| gcc called with: -g -Wall -O2 -fPIC -o tabix main.o -lm -L. -ltabix -lz | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| superenv executed: clang -pipe -w -Os -march=native -fPIC -o tabix main.o -lm -L. -ltabix -lz -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| gcc called with: -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzip.c -o bgzip.o | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang -pipe -w -Os -march=native -c -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzip.c -o bgzip.o -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| gcc called with: -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| superenv executed: clang -pipe -w -Os -march=native -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| g++ called with: -g -Wall -O2 -fPIC -c tabix.cpp | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -fPIC -c tabix.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o bgzf.o -lm -L. -ltabix -lz | |
| superenv removed: -g -Wall -O2 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| superenv executed: clang++ -pipe -w -Os -march=native -fPIC -o tabix++ main.cpp tabix.o bgzf.o -lm -L. -ltabix -lz -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| g++ called with: -c -o src/Variant.o src/Variant.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -O3 -D_FILE_OFFSET_BITS=64 | |
| superenv removed: -O3 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -c -o src/Variant.o src/Variant.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -D_FILE_OFFSET_BITS=64 -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -c -o src/split.o src/split.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -O3 -D_FILE_OFFSET_BITS=64 | |
| superenv removed: -O3 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -c -o src/split.o src/split.cpp -I. -L. -Ltabixpp/ -lvcflib -ltabix -lz -lm -D_FILE_OFFSET_BITS=64 -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -c -o smithwaterman.o smithwaterman.cpp | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -c -o smithwaterman.o smithwaterman.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -c -o Repeats.o Repeats.cpp | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -c -o Repeats.o Repeats.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -c -o LeftAlign.o LeftAlign.cpp | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -c -o LeftAlign.o LeftAlign.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -c -o IndelAllele.o IndelAllele.cpp | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -c -o IndelAllele.o IndelAllele.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -c -o disorder.o disorder.c | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| superenv executed: clang++ -pipe -w -Os -march=native -c -o disorder.o disorder.c -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers | |
| g++ called with: -Wl,-s -Wall -O3 -o smithwaterman smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o disorder.o | |
| superenv removed: -Wall -O3 | |
| superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
| superenv executed: clang++ -pipe -w -Os -march=native -Wl,-s -o smithwaterman smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o disorder.o -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
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| HOMEBREW_VERSION: 0.9.5 | |
| ORIGIN: https://github.com/Homebrew/homebrew | |
| HEAD: f6b84fbba9c441f13f4e6c2ee23e42ac5a9e38f9 | |
| Last commit: 2 days ago | |
| HOMEBREW_PREFIX: /usr/local | |
| HOMEBREW_CELLAR: /usr/local/Cellar | |
| CPU: quad-core 64-bit sandybridge | |
| OS X: 10.10.1-x86_64 | |
| Xcode: 6.1 | |
| CLT: 6.1.1.0.1.1416017670 | |
| Clang: 6.0 build 600 | |
| X11: 2.7.7 => /opt/X11 | |
| System Ruby: 2.0.0-481 | |
| Perl: /usr/bin/perl | |
| Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/bin/python2.7 | |
| Ruby: /usr/bin/ruby |
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| Warning: gettext files detected at a system prefix | |
| These files can cause compilation and link failures, especially if they | |
| are compiled with improper architectures. Consider removing these files: | |
| /usr/local/lib/libgettextlib.dylib | |
| /usr/local/lib/libintl.dylib | |
| /usr/local/include/libintl.h | |
| Please note that these warnings are just used to help the Homebrew maintainers | |
| with debugging if you file an issue. If everything you use Homebrew for is | |
| working fine: please don't worry and just ignore them. Thanks! | |
| Warning: Unbrewed dylibs were found in /usr/local/lib. | |
| If you didn't put them there on purpose they could cause problems when | |
| building Homebrew formulae, and may need to be deleted. | |
| Unexpected dylibs: | |
| /usr/local/lib/libasprintf.0.dylib | |
| /usr/local/lib/libgettextlib-0.18.dylib | |
| /usr/local/lib/libgettextpo.0.dylib | |
| /usr/local/lib/libgettextsrc-0.18.dylib | |
| /usr/local/lib/libhts.0.2.0-rc8-25-gaa68a05.dylib | |
| /usr/local/lib/libintl.8.dylib | |
| /usr/local/lib/libtcl8.5.dylib | |
| /usr/local/lib/libtk8.5.dylib | |
| Warning: Unbrewed header files were found in /usr/local/include. | |
| If you didn't put them there on purpose they could cause problems when | |
| building Homebrew formulae, and may need to be deleted. | |
| Unexpected header files: | |
| /usr/local/include/autosprintf.h | |
| /usr/local/include/gettext-po.h | |
| /usr/local/include/htslib/kstdint.h | |
| /usr/local/include/libintl.h | |
| /usr/local/include/mysql.h | |
| /usr/local/include/tcl.h | |
| /usr/local/include/tclDecls.h | |
| /usr/local/include/tclPlatDecls.h | |
| /usr/local/include/tclTomMath.h | |
| /usr/local/include/tclTomMathDecls.h | |
| /usr/local/include/tk.h | |
| /usr/local/include/tkDecls.h | |
| /usr/local/include/tkPlatDecls.h | |
| Warning: Unbrewed .la files were found in /usr/local/lib. | |
| If you didn't put them there on purpose they could cause problems when | |
| building Homebrew formulae, and may need to be deleted. | |
| Unexpected .la files: | |
| /usr/local/lib/libasprintf.la | |
| /usr/local/lib/libgettextlib.la | |
| /usr/local/lib/libgettextpo.la | |
| /usr/local/lib/libgettextsrc.la | |
| /usr/local/lib/libintl.la | |
| Warning: Unbrewed static libraries were found in /usr/local/lib. | |
| If you didn't put them there on purpose they could cause problems when | |
| building Homebrew formulae, and may need to be deleted. | |
| Unexpected static libraries: | |
| /usr/local/lib/libasprintf.a | |
| /usr/local/lib/libgettextpo.a | |
| /usr/local/lib/libintl.a | |
| /usr/local/lib/libtclstub8.5.a | |
| /usr/local/lib/libtkstub8.5.a | |
| Warning: Your Homebrew is outdated. | |
| You haven't updated for at least 24 hours. This is a long time in brewland! | |
| To update Homebrew, run `brew update`. | |
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