Skip to content

Instantly share code, notes, and snippets.

@sjackman

sjackman/01.cmake

Created March 8, 2016 00:02
Show Gist options
  • Save sjackman/2bbfcf212c555fb20505 to your computer and use it in GitHub Desktop.
Save sjackman/2bbfcf212c555fb20505 to your computer and use it in GitHub Desktop.
Download ZIP
salmon 0.6.0 build failure
Raw
01.cmake
2016-03-07 15:55:40 -0800
cmake
.
-DCMAKE_C_FLAGS_RELEASE=-DNDEBUG
-DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG
-DCMAKE_INSTALL_PREFIX=/gsc/btl/linuxbrew/Cellar/salmon/0.6.0
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_FIND_FRAMEWORK=LAST
-DCMAKE_VERBOSE_MAKEFILE=ON
-Wno-dev
-DCMAKE_BUILD_WITH_INSTALL_RPATH=1
-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=1
-- The C compiler identification is GNU 5.3.0
-- The CXX compiler identification is GNU 5.3.0
-- Check for working C compiler: /gsc/btl/linuxbrew/bin/gcc-5
-- Check for working C compiler: /gsc/btl/linuxbrew/bin/gcc-5 -- 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: /gsc/btl/linuxbrew/bin/g++-5
-- Check for working CXX compiler: /gsc/btl/linuxbrew/bin/g++-5 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Making Release build
running /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/fetchRapMap.sh 2>&1
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 128 0 128 0 0 376 0 --:--:-- --:--:-- --:--:-- 385
38 344k 38 133k 0 0 142k 0 0:00:02 --:--:-- 0:00:02 142k 100 344k 100 344k 0 0 315k 0 0:00:01 0:00:01 --:--:-- 1313k
Archive: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/rapmap.zip
aa721b14c3bac00e50782ab7c3efa101596cc6fc
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/.gitignore
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/CMakeLists.txt
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/README.md
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/TestingScripts/
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/TestingScripts/python/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/TestingScripts/python/ComputeSyntheticStats.py
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/cmake/
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/cmake/Modules/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/cmake/Modules/FindCereal.cmake
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/cmake/Modules/FindJellyfish.cmake
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/cmake/Modules/FindJemalloc.cmake
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/cmake/Modules/FindTcmalloc.cmake
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/external/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/external/libdivsufsort.zip
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/Const.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/EnumCoder.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/HitManager.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/IndexHeader.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/JFRaw.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/PairAlignmentFormatter.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/PairSequenceParser.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/RSDic.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/RSDicBuilder.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/RapMapConfig.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/RapMapFileSystem.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/RapMapIndex.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/RapMapSAIndex.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/RapMapUtils.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/SACollector.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/SASearcher.hpp
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/SIMDCompressionAndIntersection/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/SIMDCompressionAndIntersection/common.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/SIMDCompressionAndIntersection/intersection.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/ScopedTimer.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/SingleAlignmentFormatter.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/SpinLock.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/Type.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/Util.hpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/bar.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/bit_array.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/bit_macros.h
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/btree/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/btree/btree.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/btree/btree_container.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/btree/btree_map.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/btree/btree_set.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/kseq.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/macros.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/rank9b.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/sais.h
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/async_logger.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/common.h
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/async_log_helper.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/async_logger_impl.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/file_helper.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/format.cc
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/format.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/line_logger.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/log_msg.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/logger_impl.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/mpmc_bounded_q.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/null_mutex.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/os.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/pattern_formatter_impl.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/registry.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/details/spdlog_impl.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/formatter.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/logger.h
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/android_sink.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/base_sink.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/dist_sink.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/file_sinks.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/null_sink.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/ostream_sink.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/sink.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/stdout_sinks.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/sinks/syslog_sink.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/spdlog.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/spdlog/tweakme.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/stringpiece.h
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/Arg.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/ArgException.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/ArgTraits.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/CmdLine.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/CmdLineInterface.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/CmdLineOutput.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/Constraint.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/DocBookOutput.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/HelpVisitor.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/IgnoreRestVisitor.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/Makefile.am
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/Makefile.in
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/MultiArg.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/MultiSwitchArg.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/OptionalUnlabeledTracker.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/StandardTraits.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/StdOutput.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/SwitchArg.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/UnlabeledMultiArg.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/UnlabeledValueArg.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/ValueArg.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/ValuesConstraint.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/VersionVisitor.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/Visitor.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/XorHandler.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/tclap/ZshCompletionOutput.h
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/include/xxhash.h
creating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/CMakeLists.txt
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/EnumCoder.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/EnumCoderTest.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/HitManager.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RSDic.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RSDicBuilder.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RSDicBuilderTest.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RSDicTest.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RapMap.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RapMapFileSystem.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RapMapIndex.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RapMapIndexer.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RapMapMapper.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RapMapSAIndex.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RapMapSAIndexer.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RapMapSAMapper.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/RapMapUtils.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/UtilTest.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/bit_array.c
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/intersection.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/rank9b.cpp
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/sais.c
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/stringpiece.cc
inflating: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/scripts/../external/RapMap-large-index/src/xxhash.c
-- Found ZLIB: /gsc/btl/linuxbrew/lib64/libz.a (found version "1.2.8")
-- Looking for lzma_auto_decoder in /gsc/btl/linuxbrew/lib64/liblzma.a
-- Looking for lzma_auto_decoder in /gsc/btl/linuxbrew/lib64/liblzma.a - found
-- Looking for lzma_easy_encoder in /gsc/btl/linuxbrew/lib64/liblzma.a
-- Looking for lzma_easy_encoder in /gsc/btl/linuxbrew/lib64/liblzma.a - found
-- Looking for lzma_lzma_preset in /gsc/btl/linuxbrew/lib64/liblzma.a
-- Looking for lzma_lzma_preset in /gsc/btl/linuxbrew/lib64/liblzma.a - found
-- Found LibLZMA: /gsc/btl/linuxbrew/include (found version "5.2.2")
Found liblzma library: /gsc/btl/linuxbrew/lib64/liblzma.a
===========================================
-- Found BZip2: /gsc/btl/linuxbrew/lib64/libbz2.a (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
Found libbz2 library: /gsc/btl/linuxbrew/lib64/libbz2.a
===========================================
-- Boost version: 1.60.0
-- Found the following Boost libraries:
-- iostreams
-- filesystem
-- system
-- thread
-- timer
-- chrono
-- program_options
-- serialization
BOOST_INCLUDEDIR =
BOOST_LIBRARYDIR =
Boost_FOUND = 1
BOOST INCLUDE DIR = /gsc/btl/linuxbrew/include
BOOST INCLUDE DIRS = /gsc/btl/linuxbrew/include
BOOST LIB DIR = /gsc/btl/linuxbrew/lib64
BOOST LIBRAREIS = /gsc/btl/linuxbrew/lib64/libboost_iostreams-mt.a;/gsc/btl/linuxbrew/lib64/libboost_filesystem-mt.a;/gsc/btl/linuxbrew/lib64/libboost_system-mt.a;/gsc/btl/linuxbrew/lib64/libboost_thread-mt.a;/gsc/btl/linuxbrew/lib64/libboost_timer-mt.a;/gsc/btl/linuxbrew/lib64/libboost_chrono-mt.a;/gsc/btl/linuxbrew/lib64/libboost_program_options-mt.a;/gsc/btl/linuxbrew/lib64/libboost_serialization-mt.a
Build system will build libdivsufsort
==================================================================
Build system will fetch and build the Cereal serialization library
==================================================================
Build system will fetch and build BWA (for Salmon)
==================================================================
Build system will fetch and build Jellyfish
==================================================================
-- Found Intel TBB
TBB_LIBRARIES = /gsc/btl/linuxbrew/lib64/libtbb.so;/gsc/btl/linuxbrew/lib64/libtbbmalloc.so
Build system will compile libgff
==================================================================
Build system will compile Staden IOLib
==================================================================
Build system will fetch SPDLOG
==================================================================
-- Found PkgConfig: /gsc/btl/linuxbrew/bin/pkg-config (found version "0.29")
-- Could NOT find Jemalloc (missing: JEMALLOC_LIBRARY JEMALLOC_INCLUDE_DIR)
-- Not Found Tcmalloc: Tcmalloc_LIBRARY-NOTFOUND
Build system will fetch and use JEMalloc
==================================================================
Build system will fetch and build SparseHash
==================================================================
CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/
TBB_LIBRARIES = /gsc/btl/linuxbrew/lib64/libtbb.so;/gsc/btl/linuxbrew/lib64/libtbbmalloc.so
Boost_LIBRARIES = /gsc/btl/linuxbrew/lib64/libboost_iostreams-mt.a;/gsc/btl/linuxbrew/lib64/libboost_filesystem-mt.a;/gsc/btl/linuxbrew/lib64/libboost_system-mt.a;/gsc/btl/linuxbrew/lib64/libboost_thread-mt.a;/gsc/btl/linuxbrew/lib64/libboost_timer-mt.a;/gsc/btl/linuxbrew/lib64/libboost_chrono-mt.a;/gsc/btl/linuxbrew/lib64/libboost_program_options-mt.a;/gsc/btl/linuxbrew/lib64/libboost_serialization-mt.a
-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0
Raw
02.make
2016-03-07 15:55:53 -0800
make
install
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -H/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 -B/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 --check-build-system CMakeFiles/Makefile.cmake 0
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_progress_start /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/CMakeFiles /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
make -f CMakeFiles/libbwa.dir/build.make CMakeFiles/libbwa.dir/depend
make[2]: Entering directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/CMakeFiles/libbwa.dir/DependInfo.cmake --color=
Scanning dependencies of target libbwa
make[2]: Leaving directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
make -f CMakeFiles/libbwa.dir/build.make CMakeFiles/libbwa.dir/build
make[2]: Entering directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
[ 1%] Creating directories for 'libbwa'
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/install
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/tmp
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/src/libbwa-stamp
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/src/libbwa-stamp/libbwa-mkdir
[ 2%] Performing download step for 'libbwa'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external && curl -k -L https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -o bwa-master.tar.gz && mkdir -p bwa-master && tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 125 0 125 0 0 310 0 --:--:-- --:--:-- --:--:-- 318
6 219k 6 14509 0 0 15748 0 0:00:14 --:--:-- 0:00:14 15748 100 219k 100 219k 0 0 189k 0 0:00:01 0:00:01 --:--:-- 872k
bwa-0.7.12.3/.gitignore
bwa-0.7.12.3/.travis.yml
bwa-0.7.12.3/COPYING
bwa-0.7.12.3/ChangeLog
bwa-0.7.12.3/Makefile
bwa-0.7.12.3/NEWS.md
bwa-0.7.12.3/QSufSort.c
bwa-0.7.12.3/QSufSort.h
bwa-0.7.12.3/README-alt.md
bwa-0.7.12.3/README.md
bwa-0.7.12.3/bamlite.c
bwa-0.7.12.3/bamlite.h
bwa-0.7.12.3/bntseq.c
bwa-0.7.12.3/bntseq.h
bwa-0.7.12.3/bwa.1
bwa-0.7.12.3/bwa.c
bwa-0.7.12.3/bwa.h
bwa-0.7.12.3/bwakit/
bwa-0.7.12.3/bwakit/README.md
bwa-0.7.12.3/bwakit/bwa-postalt.js
bwa-0.7.12.3/bwakit/run-HLA
bwa-0.7.12.3/bwakit/run-bwamem
bwa-0.7.12.3/bwakit/run-gen-ref
bwa-0.7.12.3/bwakit/typeHLA-selctg.js
bwa-0.7.12.3/bwakit/typeHLA.js
bwa-0.7.12.3/bwakit/typeHLA.sh
bwa-0.7.12.3/bwamem.c
bwa-0.7.12.3/bwamem.h
bwa-0.7.12.3/bwamem_extra.c
bwa-0.7.12.3/bwamem_pair.c
bwa-0.7.12.3/bwape.c
bwa-0.7.12.3/bwase.c
bwa-0.7.12.3/bwase.h
bwa-0.7.12.3/bwaseqio.c
bwa-0.7.12.3/bwashm.c
bwa-0.7.12.3/bwt.c
bwa-0.7.12.3/bwt.h
bwa-0.7.12.3/bwt_gen.c
bwa-0.7.12.3/bwt_lite.c
bwa-0.7.12.3/bwt_lite.h
bwa-0.7.12.3/bwtaln.c
bwa-0.7.12.3/bwtaln.h
bwa-0.7.12.3/bwtgap.c
bwa-0.7.12.3/bwtgap.h
bwa-0.7.12.3/bwtindex.c
bwa-0.7.12.3/bwtsw2.h
bwa-0.7.12.3/bwtsw2_aux.c
bwa-0.7.12.3/bwtsw2_chain.c
bwa-0.7.12.3/bwtsw2_core.c
bwa-0.7.12.3/bwtsw2_main.c
bwa-0.7.12.3/bwtsw2_pair.c
bwa-0.7.12.3/example.c
bwa-0.7.12.3/fastmap.c
bwa-0.7.12.3/is.c
bwa-0.7.12.3/kbtree.h
bwa-0.7.12.3/khash.h
bwa-0.7.12.3/kopen.c
bwa-0.7.12.3/kseq.h
bwa-0.7.12.3/ksort.h
bwa-0.7.12.3/kstring.c
bwa-0.7.12.3/kstring.h
bwa-0.7.12.3/ksw.c
bwa-0.7.12.3/ksw.h
bwa-0.7.12.3/kthread.c
bwa-0.7.12.3/kvec.h
bwa-0.7.12.3/main.c
bwa-0.7.12.3/malloc_wrap.c
bwa-0.7.12.3/malloc_wrap.h
bwa-0.7.12.3/maxk.c
bwa-0.7.12.3/pemerge.c
bwa-0.7.12.3/qualfa2fq.pl
bwa-0.7.12.3/utils.c
bwa-0.7.12.3/utils.h
bwa-0.7.12.3/xa2multi.pl
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/src/libbwa-stamp/libbwa-download
[ 3%] No patch step for 'libbwa'
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/src/libbwa-stamp/libbwa-patch
[ 4%] No update step for 'libbwa'
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/src/libbwa-stamp/libbwa-update
[ 5%] No configure step for 'libbwa'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/src/libbwa-stamp/libbwa-configure
[ 6%] Performing build step for 'libbwa'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master && sh -c "make CC=/gsc/btl/linuxbrew/bin/gcc-5 CXX=/gsc/btl/linuxbrew/bin/g++-5"
make[3]: Entering directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master'
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
bwt_gen.c:878:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bgint_t oldInverseSa0RelativeRank = 0;
^
bwt_gen.c: In function 'BWTIncMergeBwt':
bwt_gen.c:952:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
unsigned int bitsInWordMinusBitPerChar;
^
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o
/gsc/btl/linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o
/gsc/btl/linuxbrew/bin/gcc-5 -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
make[3]: Leaving directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/src/libbwa-stamp/libbwa-build
[ 7%] Performing install step for 'libbwa'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master && sh -c "mkdir -p /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/install/lib && mkdir -p /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/install/include/bwa && cp libbwa.a /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/install/lib && cp *.h /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/install/include/bwa && cp is.c bwtindex.c bwt_gen.c QSufSort.c /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/src/"
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/bwa-master && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/src/libbwa-stamp/libbwa-install
[ 7%] Completed 'libbwa'
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/CMakeFiles
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/CMakeFiles/libbwa-complete
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libbwa-prefix/src/libbwa-stamp/libbwa-done
make[2]: Leaving directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
[ 7%] Built target libbwa
make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/depend
make[2]: Entering directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/CMakeFiles/libcereal.dir/DependInfo.cmake --color=
Scanning dependencies of target libcereal
make[2]: Leaving directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/build
make[2]: Entering directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
[ 7%] Creating directories for 'libcereal'
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2/build
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/install
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/tmp
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/src/libcereal-stamp
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/src/libcereal-stamp/libcereal-mkdir
[ 8%] Performing download step for 'libcereal'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external && curl -k -L https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz -o cereal-v1.1.2.tar.gz && tar -xzvf cereal-v1.1.2.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 122 0 122 0 0 285 0 --:--:-- --:--:-- --:--:-- 287
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 197k 100 197k 0 0 180k 0 0:00:01 0:00:01 --:--:-- 301k
cereal-1.1.2/
cereal-1.1.2/.gitignore
cereal-1.1.2/.travis.yml
cereal-1.1.2/CMakeLists.txt
cereal-1.1.2/LICENSE
cereal-1.1.2/README.md
cereal-1.1.2/doc/
cereal-1.1.2/doc/DoxygenLayout.xml
cereal-1.1.2/doc/doxygen.in
cereal-1.1.2/doc/footer.html
cereal-1.1.2/doc/mainpage.dox
cereal-1.1.2/include/
cereal-1.1.2/include/cereal/
cereal-1.1.2/include/cereal/access.hpp
cereal-1.1.2/include/cereal/archives/
cereal-1.1.2/include/cereal/archives/adapters.hpp
cereal-1.1.2/include/cereal/archives/binary.hpp
cereal-1.1.2/include/cereal/archives/json.hpp
cereal-1.1.2/include/cereal/archives/portable_binary.hpp
cereal-1.1.2/include/cereal/archives/xml.hpp
cereal-1.1.2/include/cereal/cereal.hpp
cereal-1.1.2/include/cereal/details/
cereal-1.1.2/include/cereal/details/helpers.hpp
cereal-1.1.2/include/cereal/details/polymorphic_impl.hpp
cereal-1.1.2/include/cereal/details/static_object.hpp
cereal-1.1.2/include/cereal/details/traits.hpp
cereal-1.1.2/include/cereal/details/util.hpp
cereal-1.1.2/include/cereal/external/
cereal-1.1.2/include/cereal/external/base64.hpp
cereal-1.1.2/include/cereal/external/rapidjson/
cereal-1.1.2/include/cereal/external/rapidjson/document.h
cereal-1.1.2/include/cereal/external/rapidjson/filestream.h
cereal-1.1.2/include/cereal/external/rapidjson/genericstream.h
cereal-1.1.2/include/cereal/external/rapidjson/internal/
cereal-1.1.2/include/cereal/external/rapidjson/internal/pow10.h
cereal-1.1.2/include/cereal/external/rapidjson/internal/stack.h
cereal-1.1.2/include/cereal/external/rapidjson/internal/strfunc.h
cereal-1.1.2/include/cereal/external/rapidjson/license.txt
cereal-1.1.2/include/cereal/external/rapidjson/prettywriter.h
cereal-1.1.2/include/cereal/external/rapidjson/rapidjson.h
cereal-1.1.2/include/cereal/external/rapidjson/reader.h
cereal-1.1.2/include/cereal/external/rapidjson/stringbuffer.h
cereal-1.1.2/include/cereal/external/rapidjson/writer.h
cereal-1.1.2/include/cereal/external/rapidxml/
cereal-1.1.2/include/cereal/external/rapidxml/license.txt
cereal-1.1.2/include/cereal/external/rapidxml/manual.html
cereal-1.1.2/include/cereal/external/rapidxml/rapidxml.hpp
cereal-1.1.2/include/cereal/external/rapidxml/rapidxml_iterators.hpp
cereal-1.1.2/include/cereal/external/rapidxml/rapidxml_print.hpp
cereal-1.1.2/include/cereal/external/rapidxml/rapidxml_utils.hpp
cereal-1.1.2/include/cereal/macros.hpp
cereal-1.1.2/include/cereal/types/
cereal-1.1.2/include/cereal/types/array.hpp
cereal-1.1.2/include/cereal/types/base_class.hpp
cereal-1.1.2/include/cereal/types/bitset.hpp
cereal-1.1.2/include/cereal/types/boost_variant.hpp
cereal-1.1.2/include/cereal/types/chrono.hpp
cereal-1.1.2/include/cereal/types/common.hpp
cereal-1.1.2/include/cereal/types/complex.hpp
cereal-1.1.2/include/cereal/types/deque.hpp
cereal-1.1.2/include/cereal/types/forward_list.hpp
cereal-1.1.2/include/cereal/types/list.hpp
cereal-1.1.2/include/cereal/types/map.hpp
cereal-1.1.2/include/cereal/types/memory.hpp
cereal-1.1.2/include/cereal/types/polymorphic.hpp
cereal-1.1.2/include/cereal/types/queue.hpp
cereal-1.1.2/include/cereal/types/set.hpp
cereal-1.1.2/include/cereal/types/stack.hpp
cereal-1.1.2/include/cereal/types/string.hpp
cereal-1.1.2/include/cereal/types/tuple.hpp
cereal-1.1.2/include/cereal/types/unordered_map.hpp
cereal-1.1.2/include/cereal/types/unordered_set.hpp
cereal-1.1.2/include/cereal/types/utility.hpp
cereal-1.1.2/include/cereal/types/valarray.hpp
cereal-1.1.2/include/cereal/types/vector.hpp
cereal-1.1.2/sandbox/
cereal-1.1.2/sandbox/CMakeLists.txt
cereal-1.1.2/sandbox/performance.cpp
cereal-1.1.2/sandbox/sandbox.cpp
cereal-1.1.2/sandbox/sandbox_json.cpp
cereal-1.1.2/sandbox/sandbox_rtti.cpp
cereal-1.1.2/sandbox/sandbox_shared_lib/
cereal-1.1.2/sandbox/sandbox_shared_lib/CMakeLists.txt
cereal-1.1.2/sandbox/sandbox_shared_lib/base.cpp
cereal-1.1.2/sandbox/sandbox_shared_lib/base.hpp
cereal-1.1.2/sandbox/sandbox_shared_lib/derived.cpp
cereal-1.1.2/sandbox/sandbox_shared_lib/derived.hpp
cereal-1.1.2/sandbox/sandbox_vs.cpp
cereal-1.1.2/scripts/
cereal-1.1.2/scripts/renameincludes.sh
cereal-1.1.2/scripts/updatecoverage.sh
cereal-1.1.2/scripts/updatedoc.in
cereal-1.1.2/unittests/
cereal-1.1.2/unittests/CMakeLists.txt
cereal-1.1.2/unittests/array.cpp
cereal-1.1.2/unittests/basic_string.cpp
cereal-1.1.2/unittests/bitset.cpp
cereal-1.1.2/unittests/chrono.cpp
cereal-1.1.2/unittests/common.hpp
cereal-1.1.2/unittests/complex.cpp
cereal-1.1.2/unittests/deque.cpp
cereal-1.1.2/unittests/forward_list.cpp
cereal-1.1.2/unittests/list.cpp
cereal-1.1.2/unittests/load_construct.cpp
cereal-1.1.2/unittests/map.cpp
cereal-1.1.2/unittests/memory.cpp
cereal-1.1.2/unittests/memory_cycles.cpp
cereal-1.1.2/unittests/multimap.cpp
cereal-1.1.2/unittests/multiset.cpp
cereal-1.1.2/unittests/pair.cpp
cereal-1.1.2/unittests/pod.cpp
cereal-1.1.2/unittests/polymorphic.cpp
cereal-1.1.2/unittests/portability_test.cpp
cereal-1.1.2/unittests/portable_binary_archive.cpp
cereal-1.1.2/unittests/priority_queue.cpp
cereal-1.1.2/unittests/queue.cpp
cereal-1.1.2/unittests/run_portability_test.sh
cereal-1.1.2/unittests/run_valgrind.sh
cereal-1.1.2/unittests/set.cpp
cereal-1.1.2/unittests/stack.cpp
cereal-1.1.2/unittests/structs.cpp
cereal-1.1.2/unittests/structs_minimal.cpp
cereal-1.1.2/unittests/structs_specialized.cpp
cereal-1.1.2/unittests/tuple.cpp
cereal-1.1.2/unittests/unordered_loads.cpp
cereal-1.1.2/unittests/unordered_map.cpp
cereal-1.1.2/unittests/unordered_multimap.cpp
cereal-1.1.2/unittests/unordered_multiset.cpp
cereal-1.1.2/unittests/unordered_set.cpp
cereal-1.1.2/unittests/user_data_adapters.cpp
cereal-1.1.2/unittests/valarray.cpp
cereal-1.1.2/unittests/vector.cpp
cereal-1.1.2/unittests/versioning.cpp
cereal-1.1.2/vs2013/
cereal-1.1.2/vs2013/.gitignore
cereal-1.1.2/vs2013/performance/
cereal-1.1.2/vs2013/performance/performance.vcxproj
cereal-1.1.2/vs2013/performance/performance.vcxproj.filters
cereal-1.1.2/vs2013/sandbox/
cereal-1.1.2/vs2013/sandbox/sandbox.vcxproj
cereal-1.1.2/vs2013/sandbox/sandbox.vcxproj.filters
cereal-1.1.2/vs2013/sandbox_json/
cereal-1.1.2/vs2013/sandbox_json/sandbox_json.vcxproj
cereal-1.1.2/vs2013/sandbox_json/sandbox_json.vcxproj.filters
cereal-1.1.2/vs2013/sandbox_rtti/
cereal-1.1.2/vs2013/sandbox_rtti/sandbox_rtti.vcxproj
cereal-1.1.2/vs2013/sandbox_rtti/sandbox_rtti.vcxproj.filters
cereal-1.1.2/vs2013/sandbox_vs/
cereal-1.1.2/vs2013/sandbox_vs/sandbox_vs.vcxproj
cereal-1.1.2/vs2013/sandbox_vs/sandbox_vs.vcxproj.filters
cereal-1.1.2/vs2013/sandbox_vs_dll/
cereal-1.1.2/vs2013/sandbox_vs_dll/sandbox_vs_dll.vcxproj
cereal-1.1.2/vs2013/sandbox_vs_dll/sandbox_vs_dll.vcxproj.filters
cereal-1.1.2/vs2013/unittests/
cereal-1.1.2/vs2013/unittests/main.cpp
cereal-1.1.2/vs2013/unittests/unittests.vcxproj
cereal-1.1.2/vs2013/unittests/unittests.vcxproj.filters
cereal-1.1.2/vs2013/vs2013.sln
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/src/libcereal-stamp/libcereal-download
[ 9%] No patch step for 'libcereal'
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/src/libcereal-stamp/libcereal-patch
[ 10%] Performing update step for 'libcereal'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2 && sh -c "mkdir -p /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2/build"
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2 && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/src/libcereal-stamp/libcereal-update
[ 11%] No configure step for 'libcereal'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2/build && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2/build && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/src/libcereal-stamp/libcereal-configure
[ 12%] No build step for 'libcereal'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2/build && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2/build && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/src/libcereal-stamp/libcereal-build
[ 13%] Performing install step for 'libcereal'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2/build && sh -c "mkdir -p /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/install/include && cp -r /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2/include/cereal /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/install/include"
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/cereal-1.1.2/build && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/src/libcereal-stamp/libcereal-install
[ 14%] Completed 'libcereal'
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/CMakeFiles
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/CMakeFiles/libcereal-complete
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libcereal-prefix/src/libcereal-stamp/libcereal-done
make[2]: Leaving directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
[ 14%] Built target libcereal
make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/depend
make[2]: Entering directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0 /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/CMakeFiles/libdivsufsort.dir/DependInfo.cmake --color=
Scanning dependencies of target libdivsufsort
make[2]: Leaving directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/build
make[2]: Entering directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
[ 15%] Creating directories for 'libdivsufsort'
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/libdivsufsort-master
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/libdivsufsort-master/build
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/install
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libdivsufsort-prefix/tmp
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libdivsufsort-prefix/src/libdivsufsort-stamp
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external
/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libdivsufsort-prefix/src/libdivsufsort-stamp/libdivsufsort-mkdir
[ 16%] Performing download step (verify and extract) for 'libdivsufsort'
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libdivsufsort-prefix/src/libdivsufsort-stamp/verify-libdivsufsort.cmake
-- verifying file...
file='/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/libdivsufsort.zip'
-- verifying file... warning: did not verify file - no URL_HASH specified?
cd /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external && /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libdivsufsort-prefix/src/libdivsufsort-stamp/extract-libdivsufsort.cmake
-- extracting...
src='/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/libdivsufsort.zip'
dst='/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/libdivsufsort-master'
-- extracting... [tar xfz]
CMake Error: Problem with archive_write_finish_entry(): Can't restore time
CMake Error: Problem extracting tar: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/libdivsufsort.zip
-- extracting... [error clean up]
CMake Error at /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/libdivsufsort-prefix/src/libdivsufsort-stamp/extract-libdivsufsort.cmake:33 (message):
error: extract of
'/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0/external/libdivsufsort.zip'
failed
CMakeFiles/libdivsufsort.dir/build.make:92: recipe for target 'libdivsufsort-prefix/src/libdivsufsort-stamp/libdivsufsort-download' failed
make[2]: *** [libdivsufsort-prefix/src/libdivsufsort-stamp/libdivsufsort-download] Error 1
make[2]: Leaving directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
CMakeFiles/Makefile2:144: recipe for target 'CMakeFiles/libdivsufsort.dir/all' failed
make[1]: *** [CMakeFiles/libdivsufsort.dir/all] Error 2
make[1]: Leaving directory '/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0'
Makefile:163: recipe for target 'all' failed
make: *** [all] Error 2
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Linuxbrew/linuxbrew.git
HEAD: db90b38e52a1c5e8825e2870b14096df8e9ba967
Last commit: 44 minutes ago
HOMEBREW_PREFIX: /gsc/btl/linuxbrew
HOMEBREW_REPOSITORY: /gsc/btl/linuxbrew
HOMEBREW_CELLAR: /gsc/btl/linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 24-core 64-bit arrandale
Kernel: Linux 2.6.18-371.1.2.el5 x86_64 GNU/Linux
OS: CentOS release 5.11 (Final)
OS glibc: 2.5
OS gcc: 4.1.2
Linuxbrew glibc: 2.19
Linuxbrew gcc: 5.3.0
Clang: 3.6 build 0
X11: 2.7.8 => /usr
System Ruby: 2.3.0 => /gsc/btl/linuxbrew/Cellar/ruby/2.3.0/bin/ruby
Perl: /gsc/btl/linuxbrew/bin/perl => /gsc/btl/linuxbrew/Cellar/perl/5.22.1/bin/perl
Python: /gsc/btl/linuxbrew/bin/python => /gsc/btl/linuxbrew/Cellar/python/2.7.11/bin/python2.7
Ruby: /gsc/btl/linuxbrew/bin/ruby => /gsc/btl/linuxbrew/Cellar/ruby/2.3.0/bin/ruby
Java: 1.8.0_60
CC: /gsc/btl/linuxbrew/bin/gcc-5 => /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/bin/gcc-5
CXX: /gsc/btl/linuxbrew/bin/g++-5 => /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/bin/g++-5
OBJC: /gsc/btl/linuxbrew/bin/gcc-5
OBJCXX: /gsc/btl/linuxbrew/bin/g++-5
CFLAGS: -Os -w -pipe -march=core2
CXXFLAGS: -Os -w -pipe -march=core2
CPPFLAGS: -isystem/gsc/btl/linuxbrew/include
LDFLAGS: -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib
CMAKE_PREFIX_PATH: /gsc/btl/linuxbrew
PKG_CONFIG_LIBDIR: /gsc/btl/linuxbrew/lib/pkgconfig:/gsc/btl/linuxbrew/share/pkgconfig
PATH: /gsc/btl/linuxbrew/bin:/home/sjackman/bin:/gsc/btl/linuxbrew/bin:/gsc/btl/linuxbrew/sbin:/gsc/btl/linuxbrew/Library/ENV/scm
Raw
CMakeCache.txt
# This is the CMakeCache file.
# For build in directory: /var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0
# It was generated by CMake: /gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.
########################
# EXTERNAL cache entries
########################
//Path to a file.
BZIP2_INCLUDE_DIR:PATH=/gsc/btl/linuxbrew/include
//Path to a library.
BZIP2_LIBRARY_DEBUG:FILEPATH=BZIP2_LIBRARY_DEBUG-NOTFOUND
//Path to a library.
BZIP2_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libbz2.a
//Boost chrono library (debug)
Boost_CHRONO_LIBRARY_DEBUG:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_chrono-mt.a
//Boost chrono library (release)
Boost_CHRONO_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_chrono-mt.a
//The directory containing a CMake configuration file for Boost.
Boost_DIR:PATH=Boost_DIR-NOTFOUND
//Boost filesystem library (debug)
Boost_FILESYSTEM_LIBRARY_DEBUG:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_filesystem-mt.a
//Boost filesystem library (release)
Boost_FILESYSTEM_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_filesystem-mt.a
//Path to a file.
Boost_INCLUDE_DIR:PATH=/gsc/btl/linuxbrew/include
//Boost iostreams library (debug)
Boost_IOSTREAMS_LIBRARY_DEBUG:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_iostreams-mt.a
//Boost iostreams library (release)
Boost_IOSTREAMS_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_iostreams-mt.a
//Boost library directory DEBUG
Boost_LIBRARY_DIR_DEBUG:PATH=/gsc/btl/linuxbrew/lib64
//Boost library directory RELEASE
Boost_LIBRARY_DIR_RELEASE:PATH=/gsc/btl/linuxbrew/lib64
//Boost program_options library (debug)
Boost_PROGRAM_OPTIONS_LIBRARY_DEBUG:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_program_options-mt.a
//Boost program_options library (release)
Boost_PROGRAM_OPTIONS_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_program_options-mt.a
//Boost serialization library (debug)
Boost_SERIALIZATION_LIBRARY_DEBUG:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_serialization-mt.a
//Boost serialization library (release)
Boost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_serialization-mt.a
//Boost system library (debug)
Boost_SYSTEM_LIBRARY_DEBUG:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_system-mt.a
//Boost system library (release)
Boost_SYSTEM_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_system-mt.a
//Boost thread library (debug)
Boost_THREAD_LIBRARY_DEBUG:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_thread-mt.a
//Boost thread library (release)
Boost_THREAD_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_thread-mt.a
//Boost timer library (debug)
Boost_TIMER_LIBRARY_DEBUG:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_timer-mt.a
//Boost timer library (release)
Boost_TIMER_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libboost_timer-mt.a
//Path to a program.
CMAKE_AR:FILEPATH=/gsc/btl/linuxbrew/bin/ar
//Choose the type of build, options are: None(CMAKE_CXX_FLAGS or
// CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.
CMAKE_BUILD_TYPE:STRING=Release
//No help, variable specified on the command line.
CMAKE_BUILD_WITH_INSTALL_RPATH:UNINITIALIZED=1
//Enable/Disable color output during build.
CMAKE_COLOR_MAKEFILE:BOOL=ON
//CXX compiler
CMAKE_CXX_COMPILER:FILEPATH=/gsc/btl/linuxbrew/bin/g++-5
//Flags used by the compiler during all build types.
CMAKE_CXX_FLAGS:STRING='-Os -w -pipe -march=core2 '
//Flags used by the compiler during debug builds.
CMAKE_CXX_FLAGS_DEBUG:STRING=-g
//Flags used by the compiler during release builds for minimum
// size.
CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG
//Flags used by the compiler during release builds.
CMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG
//Flags used by the compiler during release builds with debug info.
CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG
//C compiler
CMAKE_C_COMPILER:FILEPATH=/gsc/btl/linuxbrew/bin/gcc-5
//Flags used by the compiler during all build types.
CMAKE_C_FLAGS:STRING='-Os -w -pipe -march=core2 '
//Flags used by the compiler during debug builds.
CMAKE_C_FLAGS_DEBUG:STRING=-g
//Flags used by the compiler during release builds for minimum
// size.
CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG
//Flags used by the compiler during release builds.
CMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG
//Flags used by the compiler during release builds with debug info.
CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG
//Flags used by the linker.
CMAKE_EXE_LINKER_FLAGS:STRING= -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib
//Flags used by the linker during debug builds.
CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//Enable/Disable output of compile commands during generation.
CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=OFF
//No help, variable specified on the command line.
CMAKE_FIND_FRAMEWORK:UNINITIALIZED=LAST
//Install path prefix, prepended onto install directories.
CMAKE_INSTALL_PREFIX:PATH=/gsc/btl/linuxbrew/Cellar/salmon/0.6.0
//No help, variable specified on the command line.
CMAKE_INSTALL_RPATH_USE_LINK_PATH:UNINITIALIZED=1
//Path to a program.
CMAKE_LINKER:FILEPATH=/gsc/btl/linuxbrew/bin/ld
//Path to a program.
CMAKE_MAKE_PROGRAM:FILEPATH=/gsc/btl/linuxbrew/bin/make
//Flags used by the linker during the creation of modules.
CMAKE_MODULE_LINKER_FLAGS:STRING= -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib
//Flags used by the linker during debug builds.
CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//Path to a program.
CMAKE_NM:FILEPATH=/gsc/btl/linuxbrew/bin/nm
//Path to a program.
CMAKE_OBJCOPY:FILEPATH=/gsc/btl/linuxbrew/bin/objcopy
//Path to a program.
CMAKE_OBJDUMP:FILEPATH=/gsc/btl/linuxbrew/bin/objdump
//Value Computed by CMake
CMAKE_PROJECT_NAME:STATIC=Salmon
//Path to a program.
CMAKE_RANLIB:FILEPATH=/gsc/btl/linuxbrew/bin/ranlib
//Flags used by the linker during the creation of dll's.
CMAKE_SHARED_LINKER_FLAGS:STRING= -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib
//Flags used by the linker during debug builds.
CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//If set, runtime paths are not added when installing shared libraries,
// but are added when building.
CMAKE_SKIP_INSTALL_RPATH:BOOL=NO
//If set, runtime paths are not added when using shared libraries.
CMAKE_SKIP_RPATH:BOOL=NO
//Flags used by the linker during the creation of static libraries.
CMAKE_STATIC_LINKER_FLAGS:STRING=
//Flags used by the linker during debug builds.
CMAKE_STATIC_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//Path to a program.
CMAKE_STRIP:FILEPATH=/gsc/btl/linuxbrew/bin/strip
//If this value is on, makefiles will be generated without the
// .SILENT directive, and all commands will be echoed to the console
// during the make. This is useful for debugging only. With Visual
// Studio IDE projects all commands are done without /nologo.
CMAKE_VERBOSE_MAKEFILE:BOOL=ON
//Has RapMap been fetched?
FETCHED_RAPMAP:BOOL=TRUE
//Path to a file.
JEMALLOC_INCLUDE_DIR:PATH=JEMALLOC_INCLUDE_DIR-NOTFOUND
//Path to a library.
JEMALLOC_LIBRARY:FILEPATH=JEMALLOC_LIBRARY-NOTFOUND
//Path to a file.
LIBLZMA_INCLUDE_DIR:PATH=/gsc/btl/linuxbrew/include
//Path to a library.
LIBLZMA_LIBRARY:FILEPATH=/gsc/btl/linuxbrew/lib64/liblzma.a
//pkg-config executable
PKG_CONFIG_EXECUTABLE:FILEPATH=/gsc/btl/linuxbrew/bin/pkg-config
//Value Computed by CMake
Salmon_BINARY_DIR:STATIC=/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0
//Value Computed by CMake
Salmon_SOURCE_DIR:STATIC=/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0
//TBB debug library directory
TBB_DEBUG_LIBRARY_DIRS:PATH=
//Path to a file.
TBB_INCLUDE_DIR:PATH=/gsc/btl/linuxbrew/include
//TBB include directory
TBB_INCLUDE_DIRS:PATH=/gsc/btl/linuxbrew/include
//Intel TBB install directory
TBB_INSTALL_DIR:PATH=/opt/intel/tbb;/usr/local/include;/usr/include
//Path to a library.
TBB_LIBRARY:FILEPATH=/gsc/btl/linuxbrew/lib64/libtbb.so
//Path to a library.
TBB_LIBRARY_DEBUG:FILEPATH=TBB_LIBRARY_DEBUG-NOTFOUND
//TBB library directory
TBB_LIBRARY_DIRS:PATH=/gsc/btl/linuxbrew/lib64
//Path to a library.
TBB_MALLOC_LIBRARY:FILEPATH=/gsc/btl/linuxbrew/lib64/libtbbmalloc.so
//Path to a library.
TBB_MALLOC_LIBRARY_DEBUG:FILEPATH=TBB_MALLOC_LIBRARY_DEBUG-NOTFOUND
//Path to a file.
Tcmalloc_INCLUDE_DIR:PATH=Tcmalloc_INCLUDE_DIR-NOTFOUND
//Path to a library.
Tcmalloc_LIBRARY:FILEPATH=Tcmalloc_LIBRARY-NOTFOUND
//Path to a file.
ZLIB_INCLUDE_DIR:PATH=/gsc/btl/linuxbrew/include
//Path to a library.
ZLIB_LIBRARY_DEBUG:FILEPATH=ZLIB_LIBRARY_DEBUG-NOTFOUND
//Path to a library.
ZLIB_LIBRARY_RELEASE:FILEPATH=/gsc/btl/linuxbrew/lib64/libz.a
//Dependencies for target
salmon_core_LIB_DEPENDS:STATIC=
########################
# INTERNAL cache entries
########################
//ADVANCED property for variable: BZIP2_INCLUDE_DIR
BZIP2_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BZIP2_LIBRARY_DEBUG
BZIP2_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BZIP2_LIBRARY_RELEASE
BZIP2_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//Have symbol BZ2_bzCompressInit
BZIP2_NEED_PREFIX:INTERNAL=1
//ADVANCED property for variable: Boost_CHRONO_LIBRARY_DEBUG
Boost_CHRONO_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_CHRONO_LIBRARY_RELEASE
Boost_CHRONO_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_DIR
Boost_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_FILESYSTEM_LIBRARY_DEBUG
Boost_FILESYSTEM_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_FILESYSTEM_LIBRARY_RELEASE
Boost_FILESYSTEM_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_INCLUDE_DIR
Boost_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_IOSTREAMS_LIBRARY_DEBUG
Boost_IOSTREAMS_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_IOSTREAMS_LIBRARY_RELEASE
Boost_IOSTREAMS_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_LIBRARY_DIR_DEBUG
Boost_LIBRARY_DIR_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_LIBRARY_DIR_RELEASE
Boost_LIBRARY_DIR_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_PROGRAM_OPTIONS_LIBRARY_DEBUG
Boost_PROGRAM_OPTIONS_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_PROGRAM_OPTIONS_LIBRARY_RELEASE
Boost_PROGRAM_OPTIONS_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_DEBUG
Boost_SERIALIZATION_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_RELEASE
Boost_SERIALIZATION_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_SYSTEM_LIBRARY_DEBUG
Boost_SYSTEM_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_SYSTEM_LIBRARY_RELEASE
Boost_SYSTEM_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_THREAD_LIBRARY_DEBUG
Boost_THREAD_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_THREAD_LIBRARY_RELEASE
Boost_THREAD_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_TIMER_LIBRARY_DEBUG
Boost_TIMER_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Boost_TIMER_LIBRARY_RELEASE
Boost_TIMER_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_AR
CMAKE_AR-ADVANCED:INTERNAL=1
//This is the directory where this CMakeCache.txt was created
CMAKE_CACHEFILE_DIR:INTERNAL=/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0
//Major version of cmake used to create the current loaded cache
CMAKE_CACHE_MAJOR_VERSION:INTERNAL=3
//Minor version of cmake used to create the current loaded cache
CMAKE_CACHE_MINOR_VERSION:INTERNAL=4
//Patch version of cmake used to create the current loaded cache
CMAKE_CACHE_PATCH_VERSION:INTERNAL=3
//ADVANCED property for variable: CMAKE_COLOR_MAKEFILE
CMAKE_COLOR_MAKEFILE-ADVANCED:INTERNAL=1
//Path to CMake executable.
CMAKE_COMMAND:INTERNAL=/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cmake
//Path to cpack program executable.
CMAKE_CPACK_COMMAND:INTERNAL=/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/cpack
//Path to ctest program executable.
CMAKE_CTEST_COMMAND:INTERNAL=/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/ctest
//ADVANCED property for variable: CMAKE_CXX_COMPILER
CMAKE_CXX_COMPILER-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_CXX_FLAGS
CMAKE_CXX_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_CXX_FLAGS_DEBUG
CMAKE_CXX_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_CXX_FLAGS_MINSIZEREL
CMAKE_CXX_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_CXX_FLAGS_RELEASE
CMAKE_CXX_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_CXX_FLAGS_RELWITHDEBINFO
CMAKE_CXX_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_C_COMPILER
CMAKE_C_COMPILER-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_C_FLAGS
CMAKE_C_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_C_FLAGS_DEBUG
CMAKE_C_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_C_FLAGS_MINSIZEREL
CMAKE_C_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_C_FLAGS_RELEASE
CMAKE_C_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_C_FLAGS_RELWITHDEBINFO
CMAKE_C_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//Path to cache edit program executable.
CMAKE_EDIT_COMMAND:INTERNAL=/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/bin/ccmake
//Executable file format
CMAKE_EXECUTABLE_FORMAT:INTERNAL=ELF
//ADVANCED property for variable: CMAKE_EXE_LINKER_FLAGS
CMAKE_EXE_LINKER_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_EXE_LINKER_FLAGS_DEBUG
CMAKE_EXE_LINKER_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_EXE_LINKER_FLAGS_MINSIZEREL
CMAKE_EXE_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_EXE_LINKER_FLAGS_RELEASE
CMAKE_EXE_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO
CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_EXPORT_COMPILE_COMMANDS
CMAKE_EXPORT_COMPILE_COMMANDS-ADVANCED:INTERNAL=1
//Name of external makefile project generator.
CMAKE_EXTRA_GENERATOR:INTERNAL=
//Name of generator.
CMAKE_GENERATOR:INTERNAL=Unix Makefiles
//Name of generator platform.
CMAKE_GENERATOR_PLATFORM:INTERNAL=
//Name of generator toolset.
CMAKE_GENERATOR_TOOLSET:INTERNAL=
//Source directory with the top level CMakeLists.txt file for this
// project
CMAKE_HOME_DIRECTORY:INTERNAL=/var/tmp/sjackman/salmon20160307-4399-1vksuoo/salmon-0.6.0
//Install .so files without execute permission.
CMAKE_INSTALL_SO_NO_EXE:INTERNAL=0
//ADVANCED property for variable: CMAKE_LINKER
CMAKE_LINKER-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MAKE_PROGRAM
CMAKE_MAKE_PROGRAM-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS
CMAKE_MODULE_LINKER_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_DEBUG
CMAKE_MODULE_LINKER_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL
CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO
CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_NM
CMAKE_NM-ADVANCED:INTERNAL=1
//number of local generators
CMAKE_NUMBER_OF_MAKEFILES:INTERNAL=2
//ADVANCED property for variable: CMAKE_OBJCOPY
CMAKE_OBJCOPY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_OBJDUMP
CMAKE_OBJDUMP-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_RANLIB
CMAKE_RANLIB-ADVANCED:INTERNAL=1
//Path to CMake installation.
CMAKE_ROOT:INTERNAL=/gsc/btl/linuxbrew/Cellar/cmake/3.4.3/share/cmake
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_DEBUG
CMAKE_SHARED_LINKER_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL
CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_RELEASE
CMAKE_SHARED_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO
CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SKIP_INSTALL_RPATH
CMAKE_SKIP_INSTALL_RPATH-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_SKIP_RPATH
CMAKE_SKIP_RPATH-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS
CMAKE_STATIC_LINKER_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_DEBUG
CMAKE_STATIC_LINKER_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL
CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_RELEASE
CMAKE_STATIC_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO
CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_STRIP
CMAKE_STRIP-ADVANCED:INTERNAL=1
//Suppress Warnings that are meant for the author of the CMakeLists.txt
// files.
CMAKE_SUPPRESS_DEVELOPER_WARNINGS:INTERNAL=TRUE
//uname command
CMAKE_UNAME:INTERNAL=/gsc/btl/linuxbrew/bin/uname
//ADVANCED property for variable: CMAKE_VERBOSE_MAKEFILE
CMAKE_VERBOSE_MAKEFILE-ADVANCED:INTERNAL=1
//Details about finding BZip2
FIND_PACKAGE_MESSAGE_DETAILS_BZip2:INTERNAL=[/gsc/btl/linuxbrew/lib64/libbz2.a][/gsc/btl/linuxbrew/include][v1.0.6()]
//Details about finding LibLZMA
FIND_PACKAGE_MESSAGE_DETAILS_LibLZMA:INTERNAL=[/gsc/btl/linuxbrew/include][/gsc/btl/linuxbrew/lib64/liblzma.a][1][1][1][v5.2.2()]
//Details about finding PkgConfig
FIND_PACKAGE_MESSAGE_DETAILS_PkgConfig:INTERNAL=[/gsc/btl/linuxbrew/bin/pkg-config][v0.29()]
//Details about finding ZLIB
FIND_PACKAGE_MESSAGE_DETAILS_ZLIB:INTERNAL=[/gsc/btl/linuxbrew/lib64/libz.a][/gsc/btl/linuxbrew/include][v1.2.8()]
//ADVANCED property for variable: JEMALLOC_INCLUDE_DIR
JEMALLOC_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: JEMALLOC_LIBRARY
JEMALLOC_LIBRARY-ADVANCED:INTERNAL=1
//Have library /gsc/btl/linuxbrew/lib64/liblzma.a
LIBLZMA_HAS_AUTO_DECODER:INTERNAL=1
//Have library /gsc/btl/linuxbrew/lib64/liblzma.a
LIBLZMA_HAS_EASY_ENCODER:INTERNAL=1
//Have library /gsc/btl/linuxbrew/lib64/liblzma.a
LIBLZMA_HAS_LZMA_PRESET:INTERNAL=1
//ADVANCED property for variable: LIBLZMA_INCLUDE_DIR
LIBLZMA_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: LIBLZMA_LIBRARY
LIBLZMA_LIBRARY-ADVANCED:INTERNAL=1
PC_JEMALLOC_CFLAGS:INTERNAL=
PC_JEMALLOC_CFLAGS_I:INTERNAL=
PC_JEMALLOC_CFLAGS_OTHER:INTERNAL=
PC_JEMALLOC_FOUND:INTERNAL=
PC_JEMALLOC_INCLUDEDIR:INTERNAL=
PC_JEMALLOC_LIBDIR:INTERNAL=
PC_JEMALLOC_LIBS:INTERNAL=
PC_JEMALLOC_LIBS_L:INTERNAL=
PC_JEMALLOC_LIBS_OTHER:INTERNAL=
PC_JEMALLOC_LIBS_PATHS:INTERNAL=
PC_JEMALLOC_PREFIX:INTERNAL=
PC_JEMALLOC_STATIC_CFLAGS:INTERNAL=
PC_JEMALLOC_STATIC_CFLAGS_I:INTERNAL=
PC_JEMALLOC_STATIC_CFLAGS_OTHER:INTERNAL=
PC_JEMALLOC_STATIC_LIBDIR:INTERNAL=
PC_JEMALLOC_STATIC_LIBS:INTERNAL=
PC_JEMALLOC_STATIC_LIBS_L:INTERNAL=
PC_JEMALLOC_STATIC_LIBS_OTHER:INTERNAL=
PC_JEMALLOC_STATIC_LIBS_PATHS:INTERNAL=
PC_JEMALLOC_VERSION:INTERNAL=
PC_JEMALLOC_libjemalloc_INCLUDEDIR:INTERNAL=
PC_JEMALLOC_libjemalloc_LIBDIR:INTERNAL=
PC_JEMALLOC_libjemalloc_PREFIX:INTERNAL=
PC_JEMALLOC_libjemalloc_VERSION:INTERNAL=
//ADVANCED property for variable: PKG_CONFIG_EXECUTABLE
PKG_CONFIG_EXECUTABLE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: TBB_DEBUG_LIBRARY_DIRS
TBB_DEBUG_LIBRARY_DIRS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: TBB_INCLUDE_DIR
TBB_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: TBB_INCLUDE_DIRS
TBB_INCLUDE_DIRS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: TBB_INSTALL_DIR
TBB_INSTALL_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: TBB_LIBRARY
TBB_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: TBB_LIBRARY_DEBUG
TBB_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: TBB_LIBRARY_DIRS
TBB_LIBRARY_DIRS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: TBB_MALLOC_LIBRARY
TBB_MALLOC_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: TBB_MALLOC_LIBRARY_DEBUG
TBB_MALLOC_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Tcmalloc_INCLUDE_DIR
Tcmalloc_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: Tcmalloc_LIBRARY
Tcmalloc_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: ZLIB_INCLUDE_DIR
ZLIB_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: ZLIB_LIBRARY_DEBUG
ZLIB_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: ZLIB_LIBRARY_RELEASE
ZLIB_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//Last used Boost_ADDITIONAL_VERSIONS value.
_Boost_ADDITIONAL_VERSIONS_LAST:INTERNAL=1.53;1.53.0;1.54;1.55;1.56;1.57.0;1.58
//Components requested for this build tree.
_Boost_COMPONENTS_SEARCHED:INTERNAL=chrono;filesystem;iostreams;program_options;serialization;system;thread;timer
//Last used Boost_INCLUDE_DIR value.
_Boost_INCLUDE_DIR_LAST:INTERNAL=/gsc/btl/linuxbrew/include
//Last used Boost_LIBRARY_DIR_DEBUG value.
_Boost_LIBRARY_DIR_DEBUG_LAST:INTERNAL=/gsc/btl/linuxbrew/lib64
//Last used Boost_LIBRARY_DIR_RELEASE value.
_Boost_LIBRARY_DIR_RELEASE_LAST:INTERNAL=/gsc/btl/linuxbrew/lib64
//Last used Boost_NAMESPACE value.
_Boost_NAMESPACE_LAST:INTERNAL=boost
//Last used Boost_USE_MULTITHREADED value.
_Boost_USE_MULTITHREADED_LAST:INTERNAL=ON
//Last used Boost_USE_STATIC_LIBS value.
_Boost_USE_STATIC_LIBS_LAST:INTERNAL=ON
__pkg_config_checked_PC_JEMALLOC:INTERNAL=1
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment