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express (homebrew/science/express) on Mac OS X 10.11.5 - Homebrew build logs
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Homebrew build logs for homebrew/science/express on Mac OS X 10.11.5 | |
Build date: 2016-07-12 10:43:52 |
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HOMEBREW_VERSION: 0.9.9 | |
ORIGIN: https://github.com/Homebrew/brew.git | |
HEAD: 0d189fae57bad6c209b471eba9e0b254a2b40886 | |
Last commit: 4 hours ago | |
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core | |
Core tap HEAD: b142384c51438c5bf8680c77b41b32ddf8b2e99a | |
Core tap last commit: 58 minutes ago | |
HOMEBREW_PREFIX: /usr/local | |
HOMEBREW_REPOSITORY: /usr/local | |
HOMEBREW_CELLAR: /usr/local/Cellar | |
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com | |
CPU: quad-core 64-bit arrandale | |
Homebrew Ruby: 2.0.0-p648 | |
Clang: 7.3 build 703 | |
Git: 2.9.0 => /usr/local/bin/git | |
Perl: /Users/lparsons/perl5/perlbrew/perls/perl-5.14.2/bin/perl | |
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/bin/python2.7 | |
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby | |
Java: 1.8.0_45, 1.7.0_65 | |
OS X: 10.11.5-x86_64 | |
Xcode: 7.3.1 | |
CLT: 7.3.1.0.1.1461711523 | |
X11: 2.7.9 => /opt/X11 |
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Your system is ready to brew. |
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Formula: express | |
Tap: homebrew/science | |
Path: /usr/local/Library/Taps/homebrew/homebrew-science/express.rb |
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2016-07-12 10:43:08 -0400 | |
cmake | |
. | |
-DCMAKE_C_FLAGS_RELEASE=-DNDEBUG | |
-DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG | |
-DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/express/1.5.1_3 | |
-DCMAKE_BUILD_TYPE=Release | |
-DCMAKE_FIND_FRAMEWORK=LAST | |
-DCMAKE_VERBOSE_MAKEFILE=ON | |
-Wno-dev | |
-- The C compiler identification is AppleClang 7.3.0.7030031 | |
-- The CXX compiler identification is AppleClang 7.3.0.7030031 | |
-- 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 | |
-- Detecting C compile features | |
-- Detecting C compile features - 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 | |
-- Detecting CXX compile features | |
-- Detecting CXX compile features - done | |
-- Looking for pthread.h | |
-- Looking for pthread.h - found | |
-- Looking for pthread_create | |
-- Looking for pthread_create - found | |
-- Found Threads: TRUE | |
-- Boost version: 1.60.0 | |
-- Found the following Boost libraries: | |
-- thread | |
-- system | |
-- filesystem | |
-- program_options | |
-- date_time | |
-- chrono | |
-- atomic | |
-- Found GPERFTOOLS_TCMALLOC: /usr/local/lib/libtcmalloc.dylib | |
-- Found Protobuf: /usr/local/lib/libprotobuf.dylib (found version "2.6.1") | |
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.5") | |
-- Configuring done | |
-- Generating done | |
-- Build files have been written to: /tmp/express-20160712-49177-97by64/express-1.5.1-src |
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clang called with: CMakeCCompilerId.c | |
superenv added: -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
superenv executed: clang CMakeCCompilerId.c -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
clang++ called with: CMakeCXXCompilerId.cpp | |
superenv added: -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
superenv executed: clang++ CMakeCXXCompilerId.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names | |
clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -o CMakeFiles/cmTC_e838d.dir/testCCompiler.c.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/CMakeFiles/CMakeTmp/testCCompiler.c | |
superenv removed: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_e838d.dir/testCCompiler.c.o -o cmTC_e838d | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -o CMakeFiles/cmTC_ec016.dir/CMakeCCompilerABI.c.o -c /usr/local/Cellar/cmake/3.6.0/share/cmake/Modules/CMakeCCompilerABI.c | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_ec016.dir/CMakeCCompilerABI.c.o -o cmTC_ec016 | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -std=c11 -o CMakeFiles/cmTC_c929b.dir/feature_tests.c.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/CMakeFiles/feature_tests.c | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_c929b.dir/feature_tests.c.o -o cmTC_c929b | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -std=c99 -o CMakeFiles/cmTC_d71ff.dir/feature_tests.c.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/CMakeFiles/feature_tests.c | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_d71ff.dir/feature_tests.c.o -o cmTC_d71ff | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -std=c90 -o CMakeFiles/cmTC_9b043.dir/feature_tests.c.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/CMakeFiles/feature_tests.c | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_9b043.dir/feature_tests.c.o -o cmTC_9b043 | |
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clang++ called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -o CMakeFiles/cmTC_b0768.dir/testCXXCompiler.cxx.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/CMakeFiles/CMakeTmp/testCXXCompiler.cxx | |
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clang++ called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_19578.dir/feature_tests.cxx.o -o cmTC_19578 | |
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clang called with: -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_6cf8c.dir/CheckSymbolExists.c.o -o cmTC_6cf8c | |
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2016-07-12 10:43:17 -0400 | |
make | |
install | |
/usr/local/Cellar/cmake/3.6.0/bin/cmake -H/tmp/express-20160712-49177-97by64/express-1.5.1-src -B/tmp/express-20160712-49177-97by64/express-1.5.1-src --check-build-system CMakeFiles/Makefile.cmake 0 | |
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cd /tmp/express-20160712-49177-97by64/express-1.5.1-src/src && /usr/local/bin/protoc --cpp_out /tmp/express-20160712-49177-97by64/express-1.5.1-src/src -I /tmp/express-20160712-49177-97by64/express-1.5.1-src/src /tmp/express-20160712-49177-97by64/express-1.5.1-src/src/targets.proto | |
cd /tmp/express-20160712-49177-97by64/express-1.5.1-src && /usr/local/Cellar/cmake/3.6.0/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/express-20160712-49177-97by64/express-1.5.1-src /tmp/express-20160712-49177-97by64/express-1.5.1-src/src /tmp/express-20160712-49177-97by64/express-1.5.1-src /tmp/express-20160712-49177-97by64/express-1.5.1-src/src /tmp/express-20160712-49177-97by64/express-1.5.1-src/src/CMakeFiles/express.dir/DependInfo.cmake --color= | |
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[ 72%] Building CXX object src/CMakeFiles/express.dir/sequence.cpp.o | |
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cd /tmp/express-20160712-49177-97by64/express-1.5.1-src/src && /usr/local/Library/ENV/4.3/clang++ -I/usr/local/include -I/tmp/express-20160712-49177-97by64/express-1.5.1-src/bamtools/include -Wall -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -o CMakeFiles/express.dir/targets.cpp.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/src/targets.cpp | |
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[ 88%] Building CXX object src/CMakeFiles/express.dir/alignments.pb.cc.o | |
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[100%] Linking CXX executable express | |
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ld: library not found for -lprotobuf | |
clang: error: linker command failed with exit code 1 (use -v to see invocation) | |
make[2]: *** [src/express] Error 1 | |
make[1]: *** [src/CMakeFiles/express.dir/all] Error 2 | |
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clang++ called with: -I/usr/local/include -I/tmp/express-20160712-49177-97by64/express-1.5.1-src/bamtools/include -Wall -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -o CMakeFiles/express.dir/bundles.cpp.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/src/bundles.cpp | |
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clang++ called with: -I/usr/local/include -I/tmp/express-20160712-49177-97by64/express-1.5.1-src/bamtools/include -Wall -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -o CMakeFiles/express.dir/fragments.cpp.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/src/fragments.cpp | |
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clang++ called with: -I/usr/local/include -I/tmp/express-20160712-49177-97by64/express-1.5.1-src/bamtools/include -Wall -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -o CMakeFiles/express.dir/directiondetector.cpp.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/src/directiondetector.cpp | |
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clang++ called with: -I/usr/local/include -I/tmp/express-20160712-49177-97by64/express-1.5.1-src/bamtools/include -Wall -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -o CMakeFiles/express.dir/biascorrection.cpp.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/src/biascorrection.cpp | |
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clang++ called with: -I/usr/local/include -I/tmp/express-20160712-49177-97by64/express-1.5.1-src/bamtools/include -Wall -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -mmacosx-version-min=10.11 -o CMakeFiles/express.dir/mapparser.cpp.o -c /tmp/express-20160712-49177-97by64/express-1.5.1-src/src/mapparser.cpp | |
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