Created
March 8, 2016 18:11
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Save sjackman/8b0c2be77efeb9507ca3 to your computer and use it in GitHub Desktop.
salmon fails to biuld on Linuxbrew
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| 2016-03-08 17:44:52 +0000 | |
| cmake | |
| . | |
| -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG | |
| -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG | |
| -DCMAKE_INSTALL_PREFIX=/home/linuxbrew/.linuxbrew/Cellar/salmon/0.4.2 | |
| -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: /home/linuxbrew/.linuxbrew/bin/gcc-5 | |
| -- Check for working C compiler: /home/linuxbrew/.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: /home/linuxbrew/.linuxbrew/bin/g++-5 | |
| -- Check for working CXX compiler: /home/linuxbrew/.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 | |
| -- Found ZLIB: /home/linuxbrew/.linuxbrew/lib/libz.a (found version "1.2.8") | |
| -- Looking for lzma_auto_decoder in /home/linuxbrew/.linuxbrew/lib/liblzma.a | |
| -- Looking for lzma_auto_decoder in /home/linuxbrew/.linuxbrew/lib/liblzma.a - found | |
| -- Looking for lzma_easy_encoder in /home/linuxbrew/.linuxbrew/lib/liblzma.a | |
| -- Looking for lzma_easy_encoder in /home/linuxbrew/.linuxbrew/lib/liblzma.a - found | |
| -- Looking for lzma_lzma_preset in /home/linuxbrew/.linuxbrew/lib/liblzma.a | |
| -- Looking for lzma_lzma_preset in /home/linuxbrew/.linuxbrew/lib/liblzma.a - found | |
| -- Found LibLZMA: /home/linuxbrew/.linuxbrew/include (found version "5.2.2") | |
| Found liblzma library: /home/linuxbrew/.linuxbrew/lib/liblzma.a | |
| =========================================== | |
| -- Found BZip2: /home/linuxbrew/.linuxbrew/lib/libbz2.a (found version "1.0.6") | |
| -- Looking for BZ2_bzCompressInit | |
| -- Looking for BZ2_bzCompressInit - found | |
| Found libbz2 library: /home/linuxbrew/.linuxbrew/lib/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 = /home/linuxbrew/.linuxbrew/include | |
| BOOST INCLUDE DIRS = /home/linuxbrew/.linuxbrew/include | |
| BOOST LIB DIR = /home/linuxbrew/.linuxbrew/lib | |
| BOOST LIBRAREIS = /home/linuxbrew/.linuxbrew/lib/libboost_iostreams-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_filesystem-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_system-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_thread-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_timer-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_chrono-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_program_options-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_serialization-mt.a | |
| 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 = /home/linuxbrew/.linuxbrew/lib/libtbb.so;/home/linuxbrew/.linuxbrew/lib/libtbbmalloc.so | |
| Build system will compile libgff | |
| ================================================================== | |
| Build system will compile Staden IOLib | |
| ================================================================== | |
| Build system will fetch SPDLOG | |
| ================================================================== | |
| -- Found PkgConfig: /home/linuxbrew/.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 | |
| ================================================================== | |
| 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 = /home/linuxbrew/.linuxbrew/lib/libtbb.so;/home/linuxbrew/.linuxbrew/lib/libtbbmalloc.so | |
| Boost_LIBRARIES = /home/linuxbrew/.linuxbrew/lib/libboost_iostreams-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_filesystem-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_system-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_thread-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_timer-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_chrono-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_program_options-mt.a;/home/linuxbrew/.linuxbrew/lib/libboost_serialization-mt.a | |
| -- Configuring done | |
| -- Generating done | |
| -- Build files have been written to: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 |
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| 2016-03-08 17:44:53 +0000 | |
| make | |
| install | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -H/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 -B/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 --check-build-system CMakeFiles/Makefile.cmake 0 | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_progress_start /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/progress.marks | |
| make -f CMakeFiles/Makefile2 all | |
| make[1]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f CMakeFiles/libbwa.dir/build.make CMakeFiles/libbwa.dir/depend | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libbwa.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target libbwa | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f CMakeFiles/libbwa.dir/build.make CMakeFiles/libbwa.dir/build | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 1%] Creating directories for 'libbwa' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/tmp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/src/libbwa-stamp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/src/libbwa-stamp/libbwa-mkdir | |
| [ 2%] Performing download step for 'libbwa' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 125 0 125 0 0 369 0 --:--:-- --:--:-- --:--:-- 370 | |
| 100 219k 100 219k 0 0 221k 0 --:--:-- --:--:-- --:--:-- 221k | |
| 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 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/src/libbwa-stamp/libbwa-download | |
| [ 3%] No patch step for 'libbwa' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/src/libbwa-stamp/libbwa-patch | |
| [ 4%] No update step for 'libbwa' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/src/libbwa-stamp/libbwa-update | |
| [ 5%] No configure step for 'libbwa' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/src/libbwa-stamp/libbwa-configure | |
| [ 6%] Performing build step for 'libbwa' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master && sh -c "make CC=/home/linuxbrew/.linuxbrew/bin/gcc-5 CXX=/home/linuxbrew/.linuxbrew/bin/g++-5" | |
| make[3]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o | |
| /home/linuxbrew/.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 | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o | |
| /home/linuxbrew/.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; | |
| ^ | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o | |
| /home/linuxbrew/.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 `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/src/libbwa-stamp/libbwa-build | |
| [ 8%] Performing install step for 'libbwa' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master && sh -c "mkdir -p /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib && mkdir -p /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa && cp libbwa.a /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib && cp *.h /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa && cp is.c bwtindex.c bwt_gen.c QSufSort.c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/" | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/bwa-master && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/src/libbwa-stamp/libbwa-install | |
| [ 9%] Completed 'libbwa' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libbwa-complete | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libbwa-prefix/src/libbwa-stamp/libbwa-done | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 9%] Built target libbwa | |
| make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/depend | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libcereal.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target libcereal | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/build | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 10%] Creating directories for 'libcereal' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0 | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0/build | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/tmp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/libcereal-mkdir | |
| [ 11%] Performing download step (download, verify and extract) for 'libcereal' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/download-libcereal.cmake | |
| -- downloading... | |
| src='http://www.cs.cmu.edu/~robp/files/cereal-v1.0.0.tgz' | |
| dst='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-v1.0.0.tgz' | |
| timeout='none' | |
| -- [download 1% complete] | |
| -- [download 2% complete] | |
| -- [download 4% complete] | |
| -- [download 9% complete] | |
| -- [download 16% complete] | |
| -- [download 23% complete] | |
| -- [download 32% complete] | |
| -- [download 37% complete] | |
| -- [download 45% complete] | |
| -- [download 54% complete] | |
| -- [download 58% complete] | |
| -- [download 66% complete] | |
| -- [download 75% complete] | |
| -- [download 83% complete] | |
| -- [download 85% complete] | |
| -- [download 94% complete] | |
| -- [download 100% complete] | |
| -- downloading... done | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/verify-libcereal.cmake | |
| -- verifying file... | |
| file='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-v1.0.0.tgz' | |
| -- verifying file... warning: did not verify file - no URL_HASH specified? | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/extract-libcereal.cmake | |
| -- extracting... | |
| src='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-v1.0.0.tgz' | |
| dst='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0' | |
| -- extracting... [tar xfz] | |
| -- extracting... [analysis] | |
| -- extracting... [rename] | |
| -- extracting... [clean up] | |
| -- extracting... done | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/libcereal-download | |
| [ 12%] No patch step for 'libcereal' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/libcereal-patch | |
| [ 13%] Performing update step for 'libcereal' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0 && sh -c "mkdir -p /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0/build" | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/libcereal-update | |
| [ 15%] No configure step for 'libcereal' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0/build && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0/build && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/libcereal-configure | |
| [ 16%] No build step for 'libcereal' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0/build && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0/build && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/libcereal-build | |
| [ 17%] Performing install step for 'libcereal' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0/build && sh -c "mkdir -p /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include && cp -r /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0/include/cereal /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include" | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal-1.0.0/build && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/libcereal-install | |
| [ 18%] Completed 'libcereal' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libcereal-complete | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libcereal-prefix/src/libcereal-stamp/libcereal-done | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 18%] Built target libcereal | |
| make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/depend | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libgff.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target libgff | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/build | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 19%] Creating directories for 'libgff' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/tmp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/libgff-mkdir | |
| [ 20%] Performing download step (download, verify and extract) for 'libgff' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/download-libgff.cmake | |
| -- downloading... | |
| src='http://www.cs.cmu.edu/~robp/files/libgff.tgz' | |
| dst='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff.tgz' | |
| timeout='none' | |
| -- [download 3% complete] | |
| -- [download 4% complete] | |
| -- [download 9% complete] | |
| -- [download 18% complete] | |
| -- [download 27% complete] | |
| -- [download 32% complete] | |
| -- [download 49% complete] | |
| -- [download 66% complete] | |
| -- [download 70% complete] | |
| -- [download 87% complete] | |
| -- [download 100% complete] | |
| -- downloading... done | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/verify-libgff.cmake | |
| -- verifying file... | |
| file='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff.tgz' | |
| -- verifying file... warning: did not verify file - no URL_HASH specified? | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/extract-libgff.cmake | |
| -- extracting... | |
| src='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff.tgz' | |
| dst='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff' | |
| -- extracting... [tar xfz] | |
| -- extracting... [analysis] | |
| -- extracting... [rename] | |
| -- extracting... [clean up] | |
| -- extracting... done | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/libgff-download | |
| [ 22%] No patch step for 'libgff' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/libgff-patch | |
| [ 23%] Performing update step for 'libgff' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff && sh -c "mkdir -p /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build" | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/libgff-update | |
| [ 24%] Performing configure step for 'libgff' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -DCMAKE_INSTALL_PREFIX:PATH=/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install "-GUnix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff | |
| -- The C compiler identification is GNU 5.3.0 | |
| -- The CXX compiler identification is GNU 5.3.0 | |
| -- Check for working C compiler: /home/linuxbrew/.linuxbrew/bin/gcc-5 | |
| -- Check for working C compiler: /home/linuxbrew/.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: /home/linuxbrew/.linuxbrew/bin/g++-5 | |
| -- Check for working CXX compiler: /home/linuxbrew/.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 | |
| -- Configuring done | |
| -- Generating done | |
| -- Build files have been written to: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/libgff-configure | |
| [ 25%] Performing build step for 'libgff' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build && make | |
| make[3]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| make[4]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| Scanning dependencies of target gff | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| [ 8%] Building CXX object CMakeFiles/gff.dir/src/codons.cpp.o | |
| [ 16%] Building CXX object CMakeFiles/gff.dir/src/GArgs.cpp.o | |
| [ 25%] Building CXX object CMakeFiles/gff.dir/src/GBase.cpp.o | |
| [ 33%] Building CXX object CMakeFiles/gff.dir/src/gdna.cpp.o | |
| [ 41%] Building CXX object CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o | |
| [ 50%] Building CXX object CMakeFiles/gff.dir/src/GFastaIndex.cpp.o | |
| [ 58%] Building CXX object CMakeFiles/gff.dir/src/gff.cpp.o | |
| [ 66%] Building CXX object CMakeFiles/gff.dir/src/gff_utils.cpp.o | |
| [ 75%] Building CXX object CMakeFiles/gff.dir/src/GStr.cpp.o | |
| [ 83%] Linking CXX static library libgff.a | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| [ 83%] Built target gff | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| Scanning dependencies of target TestGFFParse | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| [ 91%] Building CXX object CMakeFiles/TestGFFParse.dir/src/TestGFFParse.cpp.o | |
| [100%] Linking CXX executable TestGFFParse | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| [100%] Built target TestGFFParse | |
| make[4]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| make[3]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/libgff-build | |
| [ 26%] Performing install step for 'libgff' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build && make install | |
| make[3]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| make[4]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| [ 83%] Built target gff | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| [100%] Built target TestGFFParse | |
| make[4]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| Install the project... | |
| -- Install configuration: "" | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libgff.a | |
| -- Up-to-date: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/gdna.h | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/GArgs.h | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/gff_utils.h | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/GStr.h | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/GVec.hh | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/GList.hh | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/gff.h | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/GHash.hh | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/GBase.h | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/GFastaIndex.h | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/GFaSeqGet.h | |
| -- Installing: /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/codons.h | |
| make[3]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/libgff/build && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/libgff-install | |
| [ 27%] Completed 'libgff' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libgff-complete | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libgff-prefix/src/libgff-stamp/libgff-done | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 27%] Built target libgff | |
| make -f CMakeFiles/libjellyfish.dir/build.make CMakeFiles/libjellyfish.dir/depend | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libjellyfish.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target libjellyfish | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f CMakeFiles/libjellyfish.dir/build.make CMakeFiles/libjellyfish.dir/build | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 29%] Creating directories for 'libjellyfish' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3 | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3 | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/tmp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/libjellyfish-mkdir | |
| [ 30%] Performing download step (download, verify and extract) for 'libjellyfish' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/download-libjellyfish.cmake | |
| -- downloading... | |
| src='ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz' | |
| dst='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3.tar.gz' | |
| timeout='none' | |
| -- [download 0% complete] | |
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| -- downloading... done | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/verify-libjellyfish.cmake | |
| -- verifying file... | |
| file='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3.tar.gz' | |
| -- verifying file... warning: did not verify file - no URL_HASH specified? | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/extract-libjellyfish.cmake | |
| -- extracting... | |
| src='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3.tar.gz' | |
| dst='/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3' | |
| -- extracting... [tar xfz] | |
| -- extracting... [analysis] | |
| -- extracting... [rename] | |
| -- extracting... [clean up] | |
| -- extracting... done | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/libjellyfish-download | |
| [ 31%] No patch step for 'libjellyfish' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/libjellyfish-patch | |
| [ 32%] No update step for 'libjellyfish' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/libjellyfish-update | |
| [ 33%] Performing configure step for 'libjellyfish' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3 && /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3/configure --prefix=/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install CC=/home/linuxbrew/.linuxbrew/bin/gcc-5 CXX=/home/linuxbrew/.linuxbrew/bin/g++-5 CXXFLAGS= | |
| checking build system type... x86_64-unknown-linux-gnu | |
| checking host system type... x86_64-unknown-linux-gnu | |
| checking for a BSD-compatible install... /usr/bin/install -c | |
| checking whether build environment is sane... yes | |
| checking for a thread-safe mkdir -p... /bin/mkdir -p | |
| checking for gawk... no | |
| checking for mawk... mawk | |
| checking whether make sets $(MAKE)... yes | |
| checking whether make supports nested variables... yes | |
| checking how to print strings... printf | |
| checking for style of include used by make... GNU | |
| checking for gcc... /home/linuxbrew/.linuxbrew/bin/gcc-5 | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.out | |
| checking for suffix of executables... | |
| checking whether we are cross compiling... no | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether /home/linuxbrew/.linuxbrew/bin/gcc-5 accepts -g... yes | |
| checking for /home/linuxbrew/.linuxbrew/bin/gcc-5 option to accept ISO C89... none needed | |
| checking dependency style of /home/linuxbrew/.linuxbrew/bin/gcc-5... gcc3 | |
| checking for a sed that does not truncate output... /bin/sed | |
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| checking for fgrep... /bin/grep -F | |
| checking for ld used by /home/linuxbrew/.linuxbrew/bin/gcc-5... /usr/bin/ld | |
| checking if the linker (/usr/bin/ld) is GNU ld... yes | |
| checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B | |
| checking the name lister (/usr/bin/nm -B) interface... BSD nm | |
| checking whether ln -s works... yes | |
| checking the maximum length of command line arguments... 3458764513820540925 | |
| checking whether the shell understands some XSI constructs... yes | |
| checking whether the shell understands "+="... yes | |
| checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop | |
| checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop | |
| checking for /usr/bin/ld option to reload object files... -r | |
| checking for objdump... objdump | |
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| checking command to parse /usr/bin/nm -B output from /home/linuxbrew/.linuxbrew/bin/gcc-5 object... ok | |
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| checking if mt is a manifest tool... no | |
| checking how to run the C preprocessor... /home/linuxbrew/.linuxbrew/bin/gcc-5 -E | |
| checking for ANSI C header files... yes | |
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| checking if /home/linuxbrew/.linuxbrew/bin/gcc-5 supports -c -o file.o... yes | |
| checking if /home/linuxbrew/.linuxbrew/bin/gcc-5 supports -c -o file.o... (cached) yes | |
| checking whether the /home/linuxbrew/.linuxbrew/bin/gcc-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes | |
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| checking dynamic linker characteristics... GNU/Linux ld.so | |
| checking how to hardcode library paths into programs... immediate | |
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| checking whether we are using the GNU C++ compiler... yes | |
| checking whether /home/linuxbrew/.linuxbrew/bin/g++-5 accepts -g... yes | |
| checking dependency style of /home/linuxbrew/.linuxbrew/bin/g++-5... gcc3 | |
| checking how to run the C++ preprocessor... /home/linuxbrew/.linuxbrew/bin/g++-5 -E | |
| checking for ld used by /home/linuxbrew/.linuxbrew/bin/g++-5... /usr/bin/ld -m elf_x86_64 | |
| checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes | |
| checking whether the /home/linuxbrew/.linuxbrew/bin/g++-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes | |
| checking for /home/linuxbrew/.linuxbrew/bin/g++-5 option to produce PIC... -fPIC -DPIC | |
| checking if /home/linuxbrew/.linuxbrew/bin/g++-5 PIC flag -fPIC -DPIC works... yes | |
| checking if /home/linuxbrew/.linuxbrew/bin/g++-5 static flag -static works... yes | |
| checking if /home/linuxbrew/.linuxbrew/bin/g++-5 supports -c -o file.o... yes | |
| checking if /home/linuxbrew/.linuxbrew/bin/g++-5 supports -c -o file.o... (cached) yes | |
| checking whether the /home/linuxbrew/.linuxbrew/bin/g++-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes | |
| checking dynamic linker characteristics... (cached) GNU/Linux ld.so | |
| checking how to hardcode library paths into programs... immediate | |
| checking for md5sum... md5sum | |
| checking for yaggo... false | |
| checking for pkg-config... /home/linuxbrew/.linuxbrew/bin/pkg-config | |
| checking pkg-config is at least version 0.9.0... yes | |
| checking for __int128... yes | |
| checking for std::numeric_limits<__int128>... no | |
| checking for _NSGetExecutablePath... no | |
| checking for execinfo.h... yes | |
| checking for ext/stdio_filebuf.h... yes | |
| checking for siginfo_t.si_int... yes | |
| configure: creating ./config.status | |
| config.status: creating Makefile | |
| config.status: creating tests/compat.sh | |
| config.status: creating jellyfish-2.0.pc | |
| config.status: creating config.h | |
| config.status: executing depfiles commands | |
| config.status: executing libtool commands | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/libjellyfish-configure | |
| [ 34%] Performing build step for 'libjellyfish' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3 && CC=/home/linuxbrew/.linuxbrew/bin/gcc-5 CXX=/home/linuxbrew/.linuxbrew/bin/g++-5 CXXFLAGS= | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/libjellyfish-build | |
| [ 36%] Performing install step for 'libjellyfish' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3 && make install && cp config.h /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3/jellyfish/ && cp config.h /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/ | |
| make[3]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3' | |
| make install-am | |
| make[4]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3' | |
| CXX lib/rectangular_binary_matrix.lo | |
| CXX lib/mer_dna.lo | |
| CXX lib/storage.lo | |
| CXX lib/allocators_mmap.lo | |
| CXX lib/misc.lo | |
| CXX lib/int128.lo | |
| CXX lib/thread_exec.lo | |
| CXX lib/err.lo | |
| CXX lib/jsoncpp.lo | |
| CXX lib/time.lo | |
| CXX lib/generator_manager.lo | |
| CXXLD libjellyfish-2.0.la | |
| CXX sub_commands/jellyfish.o | |
| CXX sub_commands/count_main.o | |
| sub_commands/count_main.cc: In function 'int count_main(int, char**)': | |
| sub_commands/count_main.cc:246:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] | |
| std::auto_ptr<jellyfish::dumper_t<mer_array> > dumper; | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/memory:81:0, | |
| from sub_commands/count_main.cc:28: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/unique_ptr.h:49:28: note: declared here | |
| template<typename> class auto_ptr; | |
| ^ | |
| CXX sub_commands/info_main.o | |
| CXX sub_commands/dump_main.o | |
| CXX sub_commands/histo_main.o | |
| CXX sub_commands/stats_main.o | |
| CXX sub_commands/merge_main.o | |
| CXX sub_commands/bc_main.o | |
| CXX sub_commands/query_main.o | |
| CXX sub_commands/cite_main.o | |
| CXX jellyfish/merge_files.o | |
| jellyfish/merge_files.cc:36:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] | |
| typedef std::auto_ptr<binary_reader> binary_reader_ptr; | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_conv.h:41:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/locale:43, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iomanip:43, | |
| from ./include/jellyfish/err.hpp:21, | |
| from ./jellyfish/merge_files.hpp:21, | |
| from jellyfish/merge_files.cc:17: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/unique_ptr.h:49:28: note: declared here | |
| template<typename> class auto_ptr; | |
| ^ | |
| jellyfish/merge_files.cc:37:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] | |
| typedef std::auto_ptr<text_reader> text_reader_ptr; | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_conv.h:41:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/locale:43, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iomanip:43, | |
| from ./include/jellyfish/err.hpp:21, | |
| from ./jellyfish/merge_files.hpp:21, | |
| from jellyfish/merge_files.cc:17: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/unique_ptr.h:49:28: note: declared here | |
| template<typename> class auto_ptr; | |
| ^ | |
| jellyfish/merge_files.cc:48:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] | |
| typedef std::auto_ptr<RectangularBinaryMatrix> matrix_ptr; | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_conv.h:41:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/locale:43, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iomanip:43, | |
| from ./include/jellyfish/err.hpp:21, | |
| from ./jellyfish/merge_files.hpp:21, | |
| from jellyfish/merge_files.cc:17: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/unique_ptr.h:49:28: note: declared here | |
| template<typename> class auto_ptr; | |
| ^ | |
| CXXLD bin/jellyfish | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3' | |
| /bin/mkdir -p '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib' | |
| /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib' | |
| libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libjellyfish-2.0.so.2.0.0 | |
| libtool: install: (cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) | |
| libtool: install: (cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) | |
| libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libjellyfish-2.0.la | |
| libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libjellyfish-2.0.a | |
| libtool: install: chmod 644 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libjellyfish-2.0.a | |
| libtool: install: ranlib /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libjellyfish-2.0.a | |
| libtool: finish: PATH="/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/linuxbrew/.linuxbrew/Library/ENV/scm:/sbin" ldconfig -n /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib | |
| ---------------------------------------------------------------------- | |
| Libraries have been installed in: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib | |
| If you ever happen to want to link against installed libraries | |
| in a given directory, LIBDIR, you must either use libtool, and | |
| specify the full pathname of the library, or use the `-LLIBDIR' | |
| flag during linking and do at least one of the following: | |
| - add LIBDIR to the `LD_LIBRARY_PATH' environment variable | |
| during execution | |
| - add LIBDIR to the `LD_RUN_PATH' environment variable | |
| during linking | |
| - use the `-Wl,-rpath -Wl,LIBDIR' linker flag | |
| - have your system administrator add LIBDIR to `/etc/ld.so.conf' | |
| See any operating system documentation about shared libraries for | |
| more information, such as the ld(1) and ld.so(8) manual pages. | |
| ---------------------------------------------------------------------- | |
| /bin/mkdir -p '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin' | |
| /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin' | |
| libtool: install: /usr/bin/install -c bin/.libs/jellyfish /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/jellyfish | |
| /bin/mkdir -p '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3/jellyfish' | |
| /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3/jellyfish' | |
| /usr/bin/install -c -m 644 include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3/jellyfish' | |
| /bin/mkdir -p '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man1' | |
| /usr/bin/install -c -m 644 'doc/jellyfish.man' '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man1/jellyfish.1' | |
| /bin/mkdir -p '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/pkgconfig' | |
| /usr/bin/install -c -m 644 jellyfish-2.0.pc '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/pkgconfig' | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3' | |
| make[4]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3' | |
| make[3]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jellyfish-2.1.3 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/libjellyfish-install | |
| [ 37%] Completed 'libjellyfish' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libjellyfish-complete | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjellyfish-prefix/src/libjellyfish-stamp/libjellyfish-done | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 37%] Built target libjellyfish | |
| make -f CMakeFiles/libjemalloc.dir/build.make CMakeFiles/libjemalloc.dir/depend | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libjemalloc.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target libjemalloc | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f CMakeFiles/libjemalloc.dir/build.make CMakeFiles/libjemalloc.dir/build | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 38%] Creating directories for 'libjemalloc' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0 | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0 | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/tmp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/src/libjemalloc-stamp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/src/libjemalloc-stamp/libjemalloc-mkdir | |
| [ 39%] Performing download step for 'libjemalloc' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz && tar -xzf jemalloc-3.6.0.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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 127 0 127 0 0 321 0 --:--:-- --:--:-- --:--:-- 328 | |
| 55 327k 55 182k 0 0 133k 0 0:00:02 0:00:01 0:00:01 133k 100 327k 100 327k 0 0 171k 0 0:00:01 0:00:01 --:--:-- 266k | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/src/libjemalloc-stamp/libjemalloc-download | |
| [ 40%] No patch step for 'libjemalloc' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/src/libjemalloc-stamp/libjemalloc-patch | |
| [ 41%] No update step for 'libjemalloc' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/src/libjemalloc-stamp/libjemalloc-update | |
| [ 43%] Performing configure step for 'libjemalloc' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0 && sh -c "CC=/home/linuxbrew/.linuxbrew/bin/gcc-5 ./autogen.sh --prefix=/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install" | |
| autoconf | |
| ./configure --enable-autogen --prefix=/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install | |
| checking for xsltproc... false | |
| checking for gcc... /home/linuxbrew/.linuxbrew/bin/gcc-5 | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.out | |
| checking for suffix of executables... | |
| checking whether we are cross compiling... no | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether /home/linuxbrew/.linuxbrew/bin/gcc-5 accepts -g... yes | |
| checking for /home/linuxbrew/.linuxbrew/bin/gcc-5 option to accept ISO C89... none needed | |
| checking how to run the C preprocessor... /home/linuxbrew/.linuxbrew/bin/gcc-5 -E | |
| checking for grep that handles long lines and -e... /bin/grep | |
| checking for egrep... /bin/grep -E | |
| checking for ANSI C header files... yes | |
| checking for sys/types.h... yes | |
| checking for sys/stat.h... yes | |
| checking for stdlib.h... yes | |
| checking for string.h... yes | |
| checking for memory.h... yes | |
| checking for strings.h... yes | |
| checking for inttypes.h... yes | |
| checking for stdint.h... yes | |
| checking for unistd.h... yes | |
| checking whether byte ordering is bigendian... no | |
| checking size of void *... 8 | |
| checking size of int... 4 | |
| checking size of long... 8 | |
| checking size of intmax_t... 8 | |
| checking build system type... x86_64-unknown-linux-gnu | |
| checking host system type... x86_64-unknown-linux-gnu | |
| checking whether pause instruction is compilable... yes | |
| checking whether SSE2 intrinsics is compilable... yes | |
| checking for ar... ar | |
| checking whether __attribute__ syntax is compilable... yes | |
| checking whether compiler supports -fvisibility=hidden... yes | |
| checking whether compiler supports -Werror... yes | |
| checking whether tls_model attribute is compilable... yes | |
| checking for a BSD-compatible install... /usr/bin/install -c | |
| checking for ranlib... ranlib | |
| checking for ld... /usr/bin/ld | |
| checking for autoconf... /home/linuxbrew/.linuxbrew/bin/autoconf | |
| checking for memalign... yes | |
| checking for valloc... yes | |
| checking configured backtracing method... N/A | |
| checking for sbrk... yes | |
| checking whether utrace(2) is compilable... no | |
| checking whether valgrind is compilable... no | |
| checking STATIC_PAGE_SHIFT... 12 | |
| cat: VERSION: No such file or directory | |
| checking pthread.h usability... yes | |
| checking pthread.h presence... yes | |
| checking for pthread.h... yes | |
| checking for pthread_create in -lpthread... yes | |
| checking for _malloc_thread_cleanup... no | |
| checking for _pthread_mutex_init_calloc_cb... no | |
| checking for TLS... yes | |
| checking whether a program using ffsl is compilable... yes | |
| checking whether atomic(9) is compilable... no | |
| checking whether Darwin OSAtomic*() is compilable... no | |
| checking whether to force 32-bit __sync_{add,sub}_and_fetch()... no | |
| checking whether to force 64-bit __sync_{add,sub}_and_fetch()... no | |
| checking whether Darwin OSSpin*() is compilable... no | |
| checking for stdbool.h that conforms to C99... yes | |
| checking for _Bool... yes | |
| configure: creating ./config.status | |
| config.status: creating Makefile | |
| config.status: creating doc/html.xsl | |
| config.status: creating doc/manpages.xsl | |
| config.status: creating doc/jemalloc.xml | |
| config.status: creating include/jemalloc/jemalloc_macros.h | |
| config.status: creating include/jemalloc/jemalloc_protos.h | |
| config.status: creating include/jemalloc/internal/jemalloc_internal.h | |
| config.status: creating test/test.sh | |
| config.status: creating test/include/test/jemalloc_test.h | |
| config.status: creating config.stamp | |
| config.status: creating bin/jemalloc.sh | |
| config.status: creating include/jemalloc/jemalloc_defs.h | |
| config.status: creating include/jemalloc/internal/jemalloc_internal_defs.h | |
| config.status: creating test/include/test/jemalloc_test_defs.h | |
| config.status: executing include/jemalloc/internal/private_namespace.h commands | |
| config.status: executing include/jemalloc/internal/private_unnamespace.h commands | |
| config.status: executing include/jemalloc/internal/public_symbols.txt commands | |
| config.status: executing include/jemalloc/internal/public_namespace.h commands | |
| config.status: executing include/jemalloc/internal/public_unnamespace.h commands | |
| config.status: executing include/jemalloc/internal/size_classes.h commands | |
| config.status: executing include/jemalloc/jemalloc_protos_jet.h commands | |
| config.status: executing include/jemalloc/jemalloc_rename.h commands | |
| config.status: executing include/jemalloc/jemalloc_mangle.h commands | |
| config.status: executing include/jemalloc/jemalloc_mangle_jet.h commands | |
| config.status: executing include/jemalloc/jemalloc.h commands | |
| =============================================================================== | |
| jemalloc version : | |
| library revision : 1 | |
| CC : /home/linuxbrew/.linuxbrew/bin/gcc-5 | |
| CPPFLAGS : -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT | |
| CFLAGS : -Os -w -pipe -march=core2 -fvisibility=hidden | |
| LDFLAGS : -L/home/linuxbrew/.linuxbrew/lib -Wl,--dynamic-linker=/home/linuxbrew/.linuxbrew/lib/ld.so -Wl,-rpath,/home/linuxbrew/.linuxbrew/lib | |
| EXTRA_LDFLAGS : | |
| LIBS : -lpthread | |
| RPATH_EXTRA : | |
| XSLTPROC : false | |
| XSLROOT : | |
| PREFIX : /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install | |
| BINDIR : /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin | |
| INCLUDEDIR : /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include | |
| LIBDIR : /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib | |
| DATADIR : /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share | |
| MANDIR : /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man | |
| srcroot : | |
| abs_srcroot : /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0/ | |
| objroot : | |
| abs_objroot : /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0/ | |
| JEMALLOC_PREFIX : | |
| JEMALLOC_PRIVATE_NAMESPACE | |
| : je_ | |
| install_suffix : | |
| autogen : 1 | |
| experimental : 1 | |
| cc-silence : 0 | |
| debug : 0 | |
| code-coverage : 0 | |
| stats : 1 | |
| prof : 0 | |
| prof-libunwind : 0 | |
| prof-libgcc : 0 | |
| prof-gcc : 0 | |
| tcache : 1 | |
| fill : 1 | |
| utrace : 0 | |
| valgrind : 0 | |
| xmalloc : 0 | |
| mremap : 0 | |
| munmap : 0 | |
| dss : 0 | |
| lazy_lock : 0 | |
| tls : 1 | |
| =============================================================================== | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/src/libjemalloc-stamp/libjemalloc-configure | |
| [ 44%] Performing build step for 'libjemalloc' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0 && make | |
| make[3]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/jemalloc.pic.o src/jemalloc.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/arena.pic.o src/arena.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/atomic.pic.o src/atomic.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/base.pic.o src/base.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bitmap.pic.o src/bitmap.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/chunk.pic.o src/chunk.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/chunk_dss.pic.o src/chunk_dss.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/chunk_mmap.pic.o src/chunk_mmap.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ckh.pic.o src/ckh.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ctl.pic.o src/ctl.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent.pic.o src/extent.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/hash.pic.o src/hash.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/huge.pic.o src/huge.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mb.pic.o src/mb.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mutex.pic.o src/mutex.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof.pic.o src/prof.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/quarantine.pic.o src/quarantine.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/rtree.pic.o src/rtree.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/stats.pic.o src/stats.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tcache.pic.o src/tcache.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/util.pic.o src/util.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -fPIC -DPIC -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tsd.pic.o src/tsd.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -shared -Wl,-soname,libjemalloc.so.1 -o lib/libjemalloc.so.1 src/jemalloc.pic.o src/arena.pic.o src/atomic.pic.o src/base.pic.o src/bitmap.pic.o src/chunk.pic.o src/chunk_dss.pic.o src/chunk_mmap.pic.o src/ckh.pic.o src/ctl.pic.o src/extent.pic.o src/hash.pic.o src/huge.pic.o src/mb.pic.o src/mutex.pic.o src/prof.pic.o src/quarantine.pic.o src/rtree.pic.o src/stats.pic.o src/tcache.pic.o src/util.pic.o src/tsd.pic.o -L/home/linuxbrew/.linuxbrew/lib -Wl,--dynamic-linker=/home/linuxbrew/.linuxbrew/lib/ld.so -Wl,-rpath,/home/linuxbrew/.linuxbrew/lib -lpthread | |
| ln -sf libjemalloc.so.1 lib/libjemalloc.so | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/jemalloc.o src/jemalloc.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/arena.o src/arena.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/atomic.o src/atomic.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/base.o src/base.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/bitmap.o src/bitmap.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/chunk.o src/chunk.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/chunk_dss.o src/chunk_dss.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/chunk_mmap.o src/chunk_mmap.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ckh.o src/ckh.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/ctl.o src/ctl.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/extent.o src/extent.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/hash.o src/hash.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/huge.o src/huge.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mb.o src/mb.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/mutex.o src/mutex.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/prof.o src/prof.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/quarantine.o src/quarantine.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/rtree.o src/rtree.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/stats.o src/stats.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tcache.o src/tcache.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/util.o src/util.c | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -Os -w -pipe -march=core2 -fvisibility=hidden -c -isystem/home/linuxbrew/.linuxbrew/include -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o src/tsd.o src/tsd.c | |
| ar crus lib/libjemalloc.a src/jemalloc.o src/arena.o src/atomic.o src/base.o src/bitmap.o src/chunk.o src/chunk_dss.o src/chunk_mmap.o src/ckh.o src/ctl.o src/extent.o src/hash.o src/huge.o src/mb.o src/mutex.o src/prof.o src/quarantine.o src/rtree.o src/stats.o src/tcache.o src/util.o src/tsd.o | |
| ar crus lib/libjemalloc_pic.a src/jemalloc.pic.o src/arena.pic.o src/atomic.pic.o src/base.pic.o src/bitmap.pic.o src/chunk.pic.o src/chunk_dss.pic.o src/chunk_mmap.pic.o src/ckh.pic.o src/ctl.pic.o src/extent.pic.o src/hash.pic.o src/huge.pic.o src/mb.pic.o src/mutex.pic.o src/prof.pic.o src/quarantine.pic.o src/rtree.pic.o src/stats.pic.o src/tcache.pic.o src/util.pic.o src/tsd.pic.o | |
| make[3]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/src/libjemalloc-stamp/libjemalloc-build | |
| [ 45%] Performing install step for 'libjemalloc' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0 && cp -r lib /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/ && cp -r include /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/ | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/jemalloc-3.6.0 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/src/libjemalloc-stamp/libjemalloc-install | |
| [ 46%] Completed 'libjemalloc' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libjemalloc-complete | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libjemalloc-prefix/src/libjemalloc-stamp/libjemalloc-done | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 46%] Built target libjemalloc | |
| make -f CMakeFiles/libspdlog.dir/build.make CMakeFiles/libspdlog.dir/depend | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libspdlog.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target libspdlog | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f CMakeFiles/libspdlog.dir/build.make CMakeFiles/libspdlog.dir/build | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 47%] Creating directories for 'libspdlog' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/spdlog | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/spdlog | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/tmp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/src/libspdlog-stamp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/src/libspdlog-stamp/libspdlog-mkdir | |
| [ 48%] Performing download step for 'libspdlog' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.5.tar.gz -o spdlog-v1.5.tar.gz && tar -xzf spdlog-v1.5.tar.gz && rm -fr spdlog && mv -f spdlog-1.5 spdlog | |
| % Total % Received % Xferd Average Speed Time Time Time Current | |
| Dload Upload Total Spent Left Speed | |
| 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 124 0 124 0 0 328 0 --:--:-- --:--:-- --:--:-- 329 | |
| 100 60338 0 60338 0 0 67734 0 --:--:-- --:--:-- --:--:-- 67734 | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/src/libspdlog-stamp/libspdlog-download | |
| [ 50%] No patch step for 'libspdlog' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/src/libspdlog-stamp/libspdlog-patch | |
| [ 51%] No update step for 'libspdlog' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/src/libspdlog-stamp/libspdlog-update | |
| [ 52%] No configure step for 'libspdlog' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/spdlog && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/spdlog && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/src/libspdlog-stamp/libspdlog-configure | |
| [ 53%] No build step for 'libspdlog' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/spdlog && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/spdlog && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/src/libspdlog-stamp/libspdlog-build | |
| [ 54%] Performing install step for 'libspdlog' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/spdlog && cp -r /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/spdlog/include/spdlog /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/spdlog && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/src/libspdlog-stamp/libspdlog-install | |
| [ 55%] Completed 'libspdlog' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libspdlog-complete | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libspdlog-prefix/src/libspdlog-stamp/libspdlog-done | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 55%] Built target libspdlog | |
| make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/depend | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libstadenio.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target libstadenio | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/build | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 56%] Creating directories for 'libstadenio' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/tmp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/src/libstadenio-stamp | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/src/libstadenio-stamp/libstadenio-mkdir | |
| [ 58%] Performing download step for 'libstadenio' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && curl -k -L https://github.com/COMBINE-lab/staden-io_lib/releases/download/v1.13.10/io_lib-1.13.10.tar.gz -o staden-io_lib-v1.13.10.tar.gz && mkdir -p staden-io_lib-1.13.10 && tar -xzf staden-io_lib-v1.13.10.tar.gz --strip-components=1 -C staden-io_lib-1.13.10 && rm -fr staden-io_lib && mv -f staden-io_lib-1.13.10 staden-io_lib | |
| % Total % Received % Xferd Average Speed Time Time Time Current | |
| Dload Upload Total Spent Left Speed | |
| 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 597 0 597 0 0 1723 0 --:--:-- --:--:-- --:--:-- 1735 | |
| 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 61 2052k 61 1266k 0 0 875k 0 0:00:02 0:00:01 0:00:01 1245k 100 2052k 100 2052k 0 0 1351k 0 0:00:01 0:00:01 --:--:-- 1886k | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/src/libstadenio-stamp/libstadenio-download | |
| [ 59%] No patch step for 'libstadenio' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/src/libstadenio-stamp/libstadenio-patch | |
| [ 60%] No update step for 'libstadenio' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E echo_append | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/src/libstadenio-stamp/libstadenio-update | |
| [ 61%] Performing configure step for 'libstadenio' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib && ./configure --enable-shared=no --without-libcurl --prefix=/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install LDFLAGS= CFLAGS= CC=/home/linuxbrew/.linuxbrew/bin/gcc-5 CXX=/home/linuxbrew/.linuxbrew/bin/g++-5 | |
| checking for a BSD-compatible install... /usr/bin/install -c | |
| checking whether build environment is sane... yes | |
| checking for a thread-safe mkdir -p... /bin/mkdir -p | |
| checking for gawk... no | |
| checking for mawk... mawk | |
| checking whether make sets $(MAKE)... yes | |
| checking whether to enable maintainer-specific portions of Makefiles... no | |
| checking for gcc... /home/linuxbrew/.linuxbrew/bin/gcc-5 | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.out | |
| checking for suffix of executables... | |
| checking whether we are cross compiling... no | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether /home/linuxbrew/.linuxbrew/bin/gcc-5 accepts -g... yes | |
| checking for /home/linuxbrew/.linuxbrew/bin/gcc-5 option to accept ISO C89... none needed | |
| checking for style of include used by make... GNU | |
| checking dependency style of /home/linuxbrew/.linuxbrew/bin/gcc-5... gcc3 | |
| checking build system type... x86_64-unknown-linux-gnu | |
| checking host system type... x86_64-unknown-linux-gnu | |
| checking how to print strings... printf | |
| checking for a sed that does not truncate output... /bin/sed | |
| checking for grep that handles long lines and -e... /bin/grep | |
| checking for egrep... /bin/grep -E | |
| checking for fgrep... /bin/grep -F | |
| checking for ld used by /home/linuxbrew/.linuxbrew/bin/gcc-5... /usr/bin/ld | |
| checking if the linker (/usr/bin/ld) is GNU ld... yes | |
| checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B | |
| checking the name lister (/usr/bin/nm -B) interface... BSD nm | |
| checking whether ln -s works... yes | |
| checking the maximum length of command line arguments... 3458764513820540925 | |
| checking whether the shell understands some XSI constructs... yes | |
| checking whether the shell understands "+="... yes | |
| checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop | |
| checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop | |
| checking for /usr/bin/ld option to reload object files... -r | |
| checking for objdump... objdump | |
| checking how to recognize dependent libraries... pass_all | |
| checking for dlltool... no | |
| checking how to associate runtime and link libraries... printf %s\n | |
| checking for ar... ar | |
| checking for archiver @FILE support... @ | |
| checking for strip... strip | |
| checking for ranlib... ranlib | |
| checking command to parse /usr/bin/nm -B output from /home/linuxbrew/.linuxbrew/bin/gcc-5 object... ok | |
| checking for sysroot... no | |
| checking for mt... mt | |
| checking if mt is a manifest tool... no | |
| checking how to run the C preprocessor... /home/linuxbrew/.linuxbrew/bin/gcc-5 -E | |
| checking for ANSI C header files... yes | |
| checking for sys/types.h... yes | |
| checking for sys/stat.h... yes | |
| checking for stdlib.h... yes | |
| checking for string.h... yes | |
| checking for memory.h... yes | |
| checking for strings.h... yes | |
| checking for inttypes.h... yes | |
| checking for stdint.h... yes | |
| checking for unistd.h... yes | |
| checking for dlfcn.h... yes | |
| checking for objdir... .libs | |
| checking if /home/linuxbrew/.linuxbrew/bin/gcc-5 supports -fno-rtti -fno-exceptions... no | |
| checking for /home/linuxbrew/.linuxbrew/bin/gcc-5 option to produce PIC... -fPIC -DPIC | |
| checking if /home/linuxbrew/.linuxbrew/bin/gcc-5 PIC flag -fPIC -DPIC works... yes | |
| checking if /home/linuxbrew/.linuxbrew/bin/gcc-5 static flag -static works... yes | |
| checking if /home/linuxbrew/.linuxbrew/bin/gcc-5 supports -c -o file.o... yes | |
| checking if /home/linuxbrew/.linuxbrew/bin/gcc-5 supports -c -o file.o... (cached) yes | |
| checking whether the /home/linuxbrew/.linuxbrew/bin/gcc-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes | |
| checking dynamic linker characteristics... GNU/Linux ld.so | |
| checking how to hardcode library paths into programs... immediate | |
| checking whether stripping libraries is possible... yes | |
| checking if libtool supports shared libraries... yes | |
| checking whether to build shared libraries... no | |
| checking whether to build static libraries... yes | |
| checking for inflateEnd in -lz... yes | |
| checking zlib.h usability... yes | |
| checking zlib.h presence... yes | |
| checking for zlib.h... yes | |
| checking for library containing gethostbyname... none required | |
| checking for library containing socket... none required | |
| checking for BZ2_bzBuffToBuffCompress in -lbz2... yes | |
| checking for lzma_easy_buffer_encode in -llzma... yes | |
| checking whether byte ordering is bigendian... no | |
| checking for ANSI C header files... (cached) yes | |
| checking for sys/wait.h that is POSIX.1 compatible... yes | |
| checking fcntl.h usability... yes | |
| checking fcntl.h presence... yes | |
| checking for fcntl.h... yes | |
| checking limits.h usability... yes | |
| checking limits.h presence... yes | |
| checking for limits.h... yes | |
| checking for unistd.h... (cached) yes | |
| checking for zlib.h... (cached) yes | |
| checking stdio_ext.h usability... yes | |
| checking stdio_ext.h presence... yes | |
| checking for stdio_ext.h... yes | |
| checking whether byte ordering is bigendian... (cached) no | |
| checking size of short... 2 | |
| checking size of int... 4 | |
| checking size of long... 8 | |
| checking for inline... inline | |
| checking for mode_t... yes | |
| checking for fileno... yes | |
| checking for fstat... yes | |
| checking for special C compiler options needed for large files... no | |
| checking for _FILE_OFFSET_BITS value needed for large files... no | |
| checking for _LARGEFILE_SOURCE value needed for large files... no | |
| checking for library containing pthread_join... -lpthread | |
| checking for library containing cos... -lm | |
| checking for strdup... yes | |
| checking for fsync... yes | |
| configure: creating ./config.status | |
| config.status: creating Makefile | |
| config.status: creating io_lib/Makefile | |
| config.status: creating progs/Makefile | |
| config.status: creating tests/Makefile | |
| config.status: creating io_lib-config | |
| config.status: creating io_lib/os.h | |
| config.status: creating io_lib_config.h | |
| config.status: executing depfiles commands | |
| config.status: executing libtool commands | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/src/libstadenio-stamp/libstadenio-configure | |
| [ 62%] Performing build step for 'libstadenio' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib && make CC=/home/linuxbrew/.linuxbrew/bin/gcc-5 CXX=/home/linuxbrew/.linuxbrew/bin/g++-5 | |
| make[3]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| make all-recursive | |
| make[4]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| Making all in io_lib | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/io_lib' | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-Read.lo -MD -MP -MF .deps/libstaden_read_la-Read.Tpo -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-Read.lo -MD -MP -MF .deps/libstaden_read_la-Read.Tpo -c Read.c -o libstaden_read_la-Read.o | |
| mv -f .deps/libstaden_read_la-Read.Tpo .deps/libstaden_read_la-Read.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c scf_extras.c -o libstaden_read_la-scf_extras.o | |
| mv -f .deps/libstaden_read_la-scf_extras.Tpo .deps/libstaden_read_la-scf_extras.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c translate.c -o libstaden_read_la-translate.o | |
| mv -f .deps/libstaden_read_la-translate.Tpo .deps/libstaden_read_la-translate.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c compression.c -o libstaden_read_la-compression.o | |
| mv -f .deps/libstaden_read_la-compression.Tpo .deps/libstaden_read_la-compression.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c ztr.c -o libstaden_read_la-ztr.o | |
| mv -f .deps/libstaden_read_la-ztr.Tpo .deps/libstaden_read_la-ztr.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c ztr_translate.c -o libstaden_read_la-ztr_translate.o | |
| mv -f .deps/libstaden_read_la-ztr_translate.Tpo .deps/libstaden_read_la-ztr_translate.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c deflate_interlaced.c -o libstaden_read_la-deflate_interlaced.o | |
| mv -f .deps/libstaden_read_la-deflate_interlaced.Tpo .deps/libstaden_read_la-deflate_interlaced.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-fpoint.lo -MD -MP -MF .deps/libstaden_read_la-fpoint.Tpo -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-fpoint.lo -MD -MP -MF .deps/libstaden_read_la-fpoint.Tpo -c fpoint.c -o libstaden_read_la-fpoint.o | |
| mv -f .deps/libstaden_read_la-fpoint.Tpo .deps/libstaden_read_la-fpoint.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-seqIOABI.lo -MD -MP -MF .deps/libstaden_read_la-seqIOABI.Tpo -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-seqIOABI.lo -MD -MP -MF .deps/libstaden_read_la-seqIOABI.Tpo -c seqIOABI.c -o libstaden_read_la-seqIOABI.o | |
| mv -f .deps/libstaden_read_la-seqIOABI.Tpo .deps/libstaden_read_la-seqIOABI.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-seqIOALF.lo -MD -MP -MF .deps/libstaden_read_la-seqIOALF.Tpo -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-seqIOALF.lo -MD -MP -MF .deps/libstaden_read_la-seqIOALF.Tpo -c seqIOALF.c -o libstaden_read_la-seqIOALF.o | |
| mv -f .deps/libstaden_read_la-seqIOALF.Tpo .deps/libstaden_read_la-seqIOALF.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-expFileIO.lo -MD -MP -MF .deps/libstaden_read_la-expFileIO.Tpo -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-expFileIO.lo -MD -MP -MF .deps/libstaden_read_la-expFileIO.Tpo -c expFileIO.c -o libstaden_read_la-expFileIO.o | |
| mv -f .deps/libstaden_read_la-expFileIO.Tpo .deps/libstaden_read_la-expFileIO.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-seqIOPlain.lo -MD -MP -MF .deps/libstaden_read_la-seqIOPlain.Tpo -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-seqIOPlain.lo -MD -MP -MF .deps/libstaden_read_la-seqIOPlain.Tpo -c seqIOPlain.c -o libstaden_read_la-seqIOPlain.o | |
| mv -f .deps/libstaden_read_la-seqIOPlain.Tpo .deps/libstaden_read_la-seqIOPlain.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-misc_scf.lo -MD -MP -MF .deps/libstaden_read_la-misc_scf.Tpo -c -o libstaden_read_la-misc_scf.lo `test -f 'misc_scf.c' || echo './'`misc_scf.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-misc_scf.lo -MD -MP -MF .deps/libstaden_read_la-misc_scf.Tpo -c misc_scf.c -o libstaden_read_la-misc_scf.o | |
| mv -f .deps/libstaden_read_la-misc_scf.Tpo .deps/libstaden_read_la-misc_scf.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-read_scf.lo -MD -MP -MF .deps/libstaden_read_la-read_scf.Tpo -c -o libstaden_read_la-read_scf.lo `test -f 'read_scf.c' || echo './'`read_scf.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-read_scf.lo -MD -MP -MF .deps/libstaden_read_la-read_scf.Tpo -c read_scf.c -o libstaden_read_la-read_scf.o | |
| mv -f .deps/libstaden_read_la-read_scf.Tpo .deps/libstaden_read_la-read_scf.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-write_scf.lo -MD -MP -MF .deps/libstaden_read_la-write_scf.Tpo -c -o libstaden_read_la-write_scf.lo `test -f 'write_scf.c' || echo './'`write_scf.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-write_scf.lo -MD -MP -MF .deps/libstaden_read_la-write_scf.Tpo -c write_scf.c -o libstaden_read_la-write_scf.o | |
| mv -f .deps/libstaden_read_la-write_scf.Tpo .deps/libstaden_read_la-write_scf.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-sff.lo -MD -MP -MF .deps/libstaden_read_la-sff.Tpo -c -o libstaden_read_la-sff.lo `test -f 'sff.c' || echo './'`sff.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-sff.lo -MD -MP -MF .deps/libstaden_read_la-sff.Tpo -c sff.c -o libstaden_read_la-sff.o | |
| mv -f .deps/libstaden_read_la-sff.Tpo .deps/libstaden_read_la-sff.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-srf.lo -MD -MP -MF .deps/libstaden_read_la-srf.Tpo -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-srf.lo -MD -MP -MF .deps/libstaden_read_la-srf.Tpo -c srf.c -o libstaden_read_la-srf.o | |
| mv -f .deps/libstaden_read_la-srf.Tpo .deps/libstaden_read_la-srf.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-array.lo -MD -MP -MF .deps/libstaden_read_la-array.Tpo -c -o libstaden_read_la-array.lo `test -f 'array.c' || echo './'`array.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-array.lo -MD -MP -MF .deps/libstaden_read_la-array.Tpo -c array.c -o libstaden_read_la-array.o | |
| mv -f .deps/libstaden_read_la-array.Tpo .deps/libstaden_read_la-array.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-compress.lo -MD -MP -MF .deps/libstaden_read_la-compress.Tpo -c -o libstaden_read_la-compress.lo `test -f 'compress.c' || echo './'`compress.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-compress.lo -MD -MP -MF .deps/libstaden_read_la-compress.Tpo -c compress.c -o libstaden_read_la-compress.o | |
| mv -f .deps/libstaden_read_la-compress.Tpo .deps/libstaden_read_la-compress.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-error.lo -MD -MP -MF .deps/libstaden_read_la-error.Tpo -c -o libstaden_read_la-error.lo `test -f 'error.c' || echo './'`error.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-error.lo -MD -MP -MF .deps/libstaden_read_la-error.Tpo -c error.c -o libstaden_read_la-error.o | |
| mv -f .deps/libstaden_read_la-error.Tpo .deps/libstaden_read_la-error.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-files.lo -MD -MP -MF .deps/libstaden_read_la-files.Tpo -c -o libstaden_read_la-files.lo `test -f 'files.c' || echo './'`files.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-files.lo -MD -MP -MF .deps/libstaden_read_la-files.Tpo -c files.c -o libstaden_read_la-files.o | |
| mv -f .deps/libstaden_read_la-files.Tpo .deps/libstaden_read_la-files.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-find.lo -MD -MP -MF .deps/libstaden_read_la-find.Tpo -c -o libstaden_read_la-find.lo `test -f 'find.c' || echo './'`find.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-find.lo -MD -MP -MF .deps/libstaden_read_la-find.Tpo -c find.c -o libstaden_read_la-find.o | |
| mv -f .deps/libstaden_read_la-find.Tpo .deps/libstaden_read_la-find.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-mach-io.lo -MD -MP -MF .deps/libstaden_read_la-mach-io.Tpo -c -o libstaden_read_la-mach-io.lo `test -f 'mach-io.c' || echo './'`mach-io.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-mach-io.lo -MD -MP -MF .deps/libstaden_read_la-mach-io.Tpo -c mach-io.c -o libstaden_read_la-mach-io.o | |
| mv -f .deps/libstaden_read_la-mach-io.Tpo .deps/libstaden_read_la-mach-io.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-open_trace_file.lo -MD -MP -MF .deps/libstaden_read_la-open_trace_file.Tpo -c -o libstaden_read_la-open_trace_file.lo `test -f 'open_trace_file.c' || echo './'`open_trace_file.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-open_trace_file.lo -MD -MP -MF .deps/libstaden_read_la-open_trace_file.Tpo -c open_trace_file.c -o libstaden_read_la-open_trace_file.o | |
| mv -f .deps/libstaden_read_la-open_trace_file.Tpo .deps/libstaden_read_la-open_trace_file.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-read_alloc.lo -MD -MP -MF .deps/libstaden_read_la-read_alloc.Tpo -c -o libstaden_read_la-read_alloc.lo `test -f 'read_alloc.c' || echo './'`read_alloc.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-read_alloc.lo -MD -MP -MF .deps/libstaden_read_la-read_alloc.Tpo -c read_alloc.c -o libstaden_read_la-read_alloc.o | |
| mv -f .deps/libstaden_read_la-read_alloc.Tpo .deps/libstaden_read_la-read_alloc.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-strings.lo -MD -MP -MF .deps/libstaden_read_la-strings.Tpo -c -o libstaden_read_la-strings.lo `test -f 'strings.c' || echo './'`strings.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-strings.lo -MD -MP -MF .deps/libstaden_read_la-strings.Tpo -c strings.c -o libstaden_read_la-strings.o | |
| mv -f .deps/libstaden_read_la-strings.Tpo .deps/libstaden_read_la-strings.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c -o libstaden_read_la-traceType.lo `test -f 'traceType.c' || echo './'`traceType.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c traceType.c -o libstaden_read_la-traceType.o | |
| mv -f .deps/libstaden_read_la-traceType.Tpo .deps/libstaden_read_la-traceType.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-xalloc.lo -MD -MP -MF .deps/libstaden_read_la-xalloc.Tpo -c -o libstaden_read_la-xalloc.lo `test -f 'xalloc.c' || echo './'`xalloc.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-xalloc.lo -MD -MP -MF .deps/libstaden_read_la-xalloc.Tpo -c xalloc.c -o libstaden_read_la-xalloc.o | |
| mv -f .deps/libstaden_read_la-xalloc.Tpo .deps/libstaden_read_la-xalloc.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c vlen.c -o libstaden_read_la-vlen.o | |
| mv -f .deps/libstaden_read_la-vlen.Tpo .deps/libstaden_read_la-vlen.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c hash_table.c -o libstaden_read_la-hash_table.o | |
| mv -f .deps/libstaden_read_la-hash_table.Tpo .deps/libstaden_read_la-hash_table.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o | |
| mv -f .deps/libstaden_read_la-jenkins_lookup3.Tpo .deps/libstaden_read_la-jenkins_lookup3.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c mFILE.c -o libstaden_read_la-mFILE.o | |
| mv -f .deps/libstaden_read_la-mFILE.Tpo .deps/libstaden_read_la-mFILE.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o | |
| mv -f .deps/libstaden_read_la-pooled_alloc.Tpo .deps/libstaden_read_la-pooled_alloc.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -o libstaden_read_la-bam.o | |
| mv -f .deps/libstaden_read_la-bam.Tpo .deps/libstaden_read_la-bam.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -o libstaden_read_la-sam_header.o | |
| mv -f .deps/libstaden_read_la-sam_header.Tpo .deps/libstaden_read_la-sam_header.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-arith_static.lo -MD -MP -MF .deps/libstaden_read_la-arith_static.Tpo -c -o libstaden_read_la-arith_static.lo `test -f 'arith_static.c' || echo './'`arith_static.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-arith_static.lo -MD -MP -MF .deps/libstaden_read_la-arith_static.Tpo -c arith_static.c -o libstaden_read_la-arith_static.o | |
| mv -f .deps/libstaden_read_la-arith_static.Tpo .deps/libstaden_read_la-arith_static.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c -o libstaden_read_la-rANS_static.lo `test -f 'rANS_static.c' || echo './'`rANS_static.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c rANS_static.c -o libstaden_read_la-rANS_static.o | |
| mv -f .deps/libstaden_read_la-rANS_static.Tpo .deps/libstaden_read_la-rANS_static.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -o libstaden_read_la-cram_codecs.o | |
| mv -f .deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -o libstaden_read_la-cram_encode.o | |
| mv -f .deps/libstaden_read_la-cram_encode.Tpo .deps/libstaden_read_la-cram_encode.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -o libstaden_read_la-cram_decode.o | |
| mv -f .deps/libstaden_read_la-cram_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -o libstaden_read_la-cram_stats.o | |
| mv -f .deps/libstaden_read_la-cram_stats.Tpo .deps/libstaden_read_la-cram_stats.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.o | |
| cram_io.c: In function 'cram_io_open': | |
| cram_io.c:4195:24: warning: implicit declaration of function '__fbufsize' [-Wimplicit-function-declaration] | |
| bufsize = __fbufsize(fd->fp_in); | |
| ^ | |
| mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -o libstaden_read_la-cram_index.o | |
| mv -f .deps/libstaden_read_la-cram_index.Tpo .deps/libstaden_read_la-cram_index.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -o libstaden_read_la-zfio.o | |
| mv -f .deps/libstaden_read_la-zfio.Tpo .deps/libstaden_read_la-zfio.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -o libstaden_read_la-dstring.o | |
| mv -f .deps/libstaden_read_la-dstring.Tpo .deps/libstaden_read_la-dstring.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c string_alloc.c -o libstaden_read_la-string_alloc.o | |
| mv -f .deps/libstaden_read_la-string_alloc.Tpo .deps/libstaden_read_la-string_alloc.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -o libstaden_read_la-md5.o | |
| mv -f .deps/libstaden_read_la-md5.Tpo .deps/libstaden_read_la-md5.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -o libstaden_read_la-scram.o | |
| mv -f .deps/libstaden_read_la-scram.Tpo .deps/libstaden_read_la-scram.Plo | |
| /bin/bash ../libtool --tag=CC --mode=compile /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c | |
| libtool: compile: /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -o libstaden_read_la-thread_pool.o | |
| mv -f .deps/libstaden_read_la-thread_pool.Tpo .deps/libstaden_read_la-thread_pool.Plo | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -version-info 9:1:8 -o libstaden-read.la -rpath /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-arith_static.lo libstaden_read_la-rANS_static.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo -lz -lm -lpthread -llzma -lbz2 | |
| libtool: link: ar cru .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-arith_static.o libstaden_read_la-rANS_static.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o | |
| libtool: link: ranlib .libs/libstaden-read.a | |
| libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/io_lib' | |
| Making all in progs | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/progs' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT convert_trace.o -MD -MP -MF .deps/convert_trace.Tpo -c -o convert_trace.o convert_trace.c | |
| mv -f .deps/convert_trace.Tpo .deps/convert_trace.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT makeSCF.o -MD -MP -MF .deps/makeSCF.Tpo -c -o makeSCF.o makeSCF.c | |
| mv -f .deps/makeSCF.Tpo .deps/makeSCF.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT extract_seq.o -MD -MP -MF .deps/extract_seq.Tpo -c -o extract_seq.o extract_seq.c | |
| mv -f .deps/extract_seq.Tpo .deps/extract_seq.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o extract_seq extract_seq.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT extract_qual.o -MD -MP -MF .deps/extract_qual.Tpo -c -o extract_qual.o extract_qual.c | |
| mv -f .deps/extract_qual.Tpo .deps/extract_qual.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o extract_qual extract_qual.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT extract_fastq.o -MD -MP -MF .deps/extract_fastq.Tpo -c -o extract_fastq.o extract_fastq.c | |
| mv -f .deps/extract_fastq.Tpo .deps/extract_fastq.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o extract_fastq extract_fastq.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o extract_fastq extract_fastq.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT index_tar.o -MD -MP -MF .deps/index_tar.Tpo -c -o index_tar.o index_tar.c | |
| mv -f .deps/index_tar.Tpo .deps/index_tar.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o index_tar index_tar.o -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o index_tar index_tar.o -lm -lpthread -llzma -lbz2 | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT scf_dump.o -MD -MP -MF .deps/scf_dump.Tpo -c -o scf_dump.o scf_dump.c | |
| mv -f .deps/scf_dump.Tpo .deps/scf_dump.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scf_dump scf_dump.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT scf_info.o -MD -MP -MF .deps/scf_info.Tpo -c -o scf_info.o scf_info.c | |
| mv -f .deps/scf_info.Tpo .deps/scf_info.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scf_info scf_info.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scf_info scf_info.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT scf_update.o -MD -MP -MF .deps/scf_update.Tpo -c -o scf_update.o scf_update.c | |
| mv -f .deps/scf_update.Tpo .deps/scf_update.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scf_update scf_update.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scf_update scf_update.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT get_comment.o -MD -MP -MF .deps/get_comment.Tpo -c -o get_comment.o get_comment.c | |
| mv -f .deps/get_comment.Tpo .deps/get_comment.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o get_comment get_comment.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o get_comment get_comment.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT hash_tar.o -MD -MP -MF .deps/hash_tar.Tpo -c -o hash_tar.o hash_tar.c | |
| mv -f .deps/hash_tar.Tpo .deps/hash_tar.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_tar hash_tar.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT hash_extract.o -MD -MP -MF .deps/hash_extract.Tpo -c -o hash_extract.o hash_extract.c | |
| mv -f .deps/hash_extract.Tpo .deps/hash_extract.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_extract hash_extract.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT hash_list.o -MD -MP -MF .deps/hash_list.Tpo -c -o hash_list.o hash_list.c | |
| mv -f .deps/hash_list.Tpo .deps/hash_list.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_list hash_list.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_list hash_list.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT trace_dump.o -MD -MP -MF .deps/trace_dump.Tpo -c -o trace_dump.o trace_dump.c | |
| mv -f .deps/trace_dump.Tpo .deps/trace_dump.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o trace_dump trace_dump.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT hash_sff.o -MD -MP -MF .deps/hash_sff.Tpo -c -o hash_sff.o hash_sff.c | |
| mv -f .deps/hash_sff.Tpo .deps/hash_sff.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_sff hash_sff.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_sff hash_sff.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT append_sff.o -MD -MP -MF .deps/append_sff.Tpo -c -o append_sff.o append_sff.c | |
| mv -f .deps/append_sff.Tpo .deps/append_sff.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o append_sff append_sff.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o append_sff append_sff.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT ztr_dump.o -MD -MP -MF .deps/ztr_dump.Tpo -c -o ztr_dump.o ztr_dump.c | |
| mv -f .deps/ztr_dump.Tpo .deps/ztr_dump.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o ztr_dump ztr_dump.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o ztr_dump ztr_dump.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT srf_dump_all.o -MD -MP -MF .deps/srf_dump_all.Tpo -c -o srf_dump_all.o srf_dump_all.c | |
| mv -f .deps/srf_dump_all.Tpo .deps/srf_dump_all.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_dump_all srf_dump_all.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_dump_all srf_dump_all.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT srf_index_hash.o -MD -MP -MF .deps/srf_index_hash.Tpo -c -o srf_index_hash.o srf_index_hash.c | |
| mv -f .deps/srf_index_hash.Tpo .deps/srf_index_hash.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_index_hash srf_index_hash.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_index_hash srf_index_hash.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT srf_extract_linear.o -MD -MP -MF .deps/srf_extract_linear.Tpo -c -o srf_extract_linear.o srf_extract_linear.c | |
| mv -f .deps/srf_extract_linear.Tpo .deps/srf_extract_linear.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_extract_linear srf_extract_linear.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_extract_linear srf_extract_linear.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT srf_extract_hash.o -MD -MP -MF .deps/srf_extract_hash.Tpo -c -o srf_extract_hash.o srf_extract_hash.c | |
| mv -f .deps/srf_extract_hash.Tpo .deps/srf_extract_hash.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_extract_hash srf_extract_hash.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_extract_hash srf_extract_hash.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT srf2fastq.o -MD -MP -MF .deps/srf2fastq.Tpo -c -o srf2fastq.o srf2fastq.c | |
| mv -f .deps/srf2fastq.Tpo .deps/srf2fastq.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf2fastq srf2fastq.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf2fastq srf2fastq.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT srf2fasta.o -MD -MP -MF .deps/srf2fasta.Tpo -c -o srf2fasta.o srf2fasta.c | |
| mv -f .deps/srf2fasta.Tpo .deps/srf2fasta.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf2fasta srf2fasta.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf2fasta srf2fasta.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT srf_filter.o -MD -MP -MF .deps/srf_filter.Tpo -c -o srf_filter.o srf_filter.c | |
| mv -f .deps/srf_filter.Tpo .deps/srf_filter.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_filter srf_filter.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT srf_info.o -MD -MP -MF .deps/srf_info.Tpo -c -o srf_info.o srf_info.c | |
| mv -f .deps/srf_info.Tpo .deps/srf_info.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_info srf_info.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT srf_list.o -MD -MP -MF .deps/srf_list.Tpo -c -o srf_list.o srf_list.c | |
| mv -f .deps/srf_list.Tpo .deps/srf_list.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o srf_list srf_list.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT hash_exp.o -MD -MP -MF .deps/hash_exp.Tpo -c -o hash_exp.o hash_exp.c | |
| mv -f .deps/hash_exp.Tpo .deps/hash_exp.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o hash_exp hash_exp.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT cram_dump.o -MD -MP -MF .deps/cram_dump.Tpo -c -o cram_dump.o cram_dump.c | |
| cram_dump.c: In function 'DumpMap2': | |
| cram_dump.c:73:22: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] | |
| HashTableAdd(ds_h, (char *)k, 4, hd, NULL); | |
| ^ | |
| cram_dump.c: In function 'main': | |
| cram_dump.c:170:12: warning: type defaults to 'int' in declaration of 'bmax' [-Wimplicit-int] | |
| static bmax = 0; | |
| ^ | |
| cram_dump.c:299:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] | |
| hi = HashTableSearch(bsize_h, (char *)k, 4); | |
| ^ | |
| cram_dump.c:305:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] | |
| HashTableAdd(bsize_h, (char *)k, 4, hd, NULL); | |
| ^ | |
| cram_dump.c:740:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] | |
| if (!(hi = HashTableSearch(bsize_h, (char *)id, 4))) | |
| ^ | |
| cram_dump.c:743:10: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| k = (int)hi->key; | |
| ^ | |
| cram_dump.c:780:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| c = ((int)hi->key)>>8; | |
| ^ | |
| mv -f .deps/cram_dump.Tpo .deps/cram_dump.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o cram_dump cram_dump.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT cram_index.o -MD -MP -MF .deps/cram_index.Tpo -c -o cram_index.o cram_index.c | |
| mv -f .deps/cram_index.Tpo .deps/cram_index.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o cram_index cram_index.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT scramble.o -MD -MP -MF .deps/scramble.Tpo -c -o scramble.o scramble.c | |
| mv -f .deps/scramble.Tpo .deps/scramble.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scramble scramble.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scramble scramble.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT scram_merge.o -MD -MP -MF .deps/scram_merge.Tpo -c -o scram_merge.o scram_merge.c | |
| mv -f .deps/scram_merge.Tpo .deps/scram_merge.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT scram_pileup.o -MD -MP -MF .deps/scram_pileup.Tpo -c -o scram_pileup.o scram_pileup.c | |
| mv -f .deps/scram_pileup.Tpo .deps/scram_pileup.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT scram_flagstat.o -MD -MP -MF .deps/scram_flagstat.Tpo -c -o scram_flagstat.o scram_flagstat.c | |
| mv -f .deps/scram_flagstat.Tpo .deps/scram_flagstat.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT scram_test.o -MD -MP -MF .deps/scram_test.Tpo -c -o scram_test.o scram_test.c | |
| mv -f .deps/scram_test.Tpo .deps/scram_test.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o scram_test scram_test.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/progs' | |
| Making all in tests | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/tests' | |
| /home/linuxbrew/.linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I.. -isystem/home/linuxbrew/.linuxbrew/include -MT cram_io_test.o -MD -MP -MF .deps/cram_io_test.Tpo -c -o cram_io_test.o cram_io_test.c | |
| mv -f .deps/cram_io_test.Tpo .deps/cram_io_test.Po | |
| /bin/bash ../libtool --tag=CC --mode=link /home/linuxbrew/.linuxbrew/bin/gcc-5 -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 | |
| libtool: link: /home/linuxbrew/.linuxbrew/bin/gcc-5 -o cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.a -lz -lm -lpthread -llzma -lbz2 | |
| ../io_lib/.libs/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/tests' | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| make[5]: Nothing to be done for `all-am'. | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| make[4]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| make[3]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/src/libstadenio-stamp/libstadenio-build | |
| [ 63%] Performing install step for 'libstadenio' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib && make install | |
| make[3]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| Making install in io_lib | |
| make[4]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/io_lib' | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/io_lib' | |
| test -z "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib" || /bin/mkdir -p "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib" | |
| /bin/bash ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib' | |
| libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libstaden-read.la | |
| libtool: install: /usr/bin/install -c .libs/libstaden-read.a /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libstaden-read.a | |
| libtool: install: chmod 644 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libstaden-read.a | |
| libtool: install: ranlib /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib/libstaden-read.a | |
| libtool: finish: PATH="/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/linuxbrew/.linuxbrew/Library/ENV/scm:/sbin" ldconfig -n /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib | |
| ---------------------------------------------------------------------- | |
| Libraries have been installed in: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib | |
| If you ever happen to want to link against installed libraries | |
| in a given directory, LIBDIR, you must either use libtool, and | |
| specify the full pathname of the library, or use the `-LLIBDIR' | |
| flag during linking and do at least one of the following: | |
| - add LIBDIR to the `LD_LIBRARY_PATH' environment variable | |
| during execution | |
| - add LIBDIR to the `LD_RUN_PATH' environment variable | |
| during linking | |
| - use the `-Wl,-rpath -Wl,LIBDIR' linker flag | |
| - have your system administrator add LIBDIR to `/etc/ld.so.conf' | |
| See any operating system documentation about shared libraries for | |
| more information, such as the ld(1) and ld.so(8) manual pages. | |
| ---------------------------------------------------------------------- | |
| make[5]: Nothing to be done for `install-data-am'. | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/io_lib' | |
| make[4]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/io_lib' | |
| Making install in progs | |
| make[4]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/progs' | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/progs' | |
| test -z "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin" || /bin/mkdir -p "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin" | |
| /bin/bash ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin' | |
| libtool: install: /usr/bin/install -c convert_trace /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/convert_trace | |
| libtool: install: /usr/bin/install -c makeSCF /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/makeSCF | |
| libtool: install: /usr/bin/install -c extract_seq /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/extract_seq | |
| libtool: install: /usr/bin/install -c extract_qual /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/extract_qual | |
| libtool: install: /usr/bin/install -c extract_fastq /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/extract_fastq | |
| libtool: install: /usr/bin/install -c index_tar /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/index_tar | |
| libtool: install: /usr/bin/install -c scf_dump /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/scf_dump | |
| libtool: install: /usr/bin/install -c scf_info /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/scf_info | |
| libtool: install: /usr/bin/install -c scf_update /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/scf_update | |
| libtool: install: /usr/bin/install -c get_comment /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/get_comment | |
| libtool: install: /usr/bin/install -c hash_tar /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/hash_tar | |
| libtool: install: /usr/bin/install -c hash_extract /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/hash_extract | |
| libtool: install: /usr/bin/install -c hash_list /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/hash_list | |
| libtool: install: /usr/bin/install -c trace_dump /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/trace_dump | |
| libtool: install: /usr/bin/install -c hash_sff /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/hash_sff | |
| libtool: install: /usr/bin/install -c append_sff /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/append_sff | |
| libtool: install: /usr/bin/install -c ztr_dump /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/ztr_dump | |
| libtool: install: /usr/bin/install -c srf_dump_all /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/srf_dump_all | |
| libtool: install: /usr/bin/install -c srf_index_hash /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/srf_index_hash | |
| libtool: install: /usr/bin/install -c srf_extract_linear /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/srf_extract_linear | |
| libtool: install: /usr/bin/install -c srf_extract_hash /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/srf_extract_hash | |
| libtool: install: /usr/bin/install -c srf2fastq /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/srf2fastq | |
| libtool: install: /usr/bin/install -c srf2fasta /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/srf2fasta | |
| libtool: install: /usr/bin/install -c srf_filter /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/srf_filter | |
| libtool: install: /usr/bin/install -c srf_info /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/srf_info | |
| libtool: install: /usr/bin/install -c srf_list /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/srf_list | |
| libtool: install: /usr/bin/install -c hash_exp /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/hash_exp | |
| libtool: install: /usr/bin/install -c cram_dump /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/cram_dump | |
| libtool: install: /usr/bin/install -c cram_index /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/cram_index | |
| libtool: install: /usr/bin/install -c scramble /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/scramble | |
| libtool: install: /usr/bin/install -c scram_merge /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/scram_merge | |
| libtool: install: /usr/bin/install -c scram_pileup /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/scram_pileup | |
| libtool: install: /usr/bin/install -c scram_flagstat /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/scram_flagstat | |
| libtool: install: /usr/bin/install -c scram_test /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin/scram_test | |
| make[5]: Nothing to be done for `install-data-am'. | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/progs' | |
| make[4]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/progs' | |
| Making install in tests | |
| make[4]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/tests' | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/tests' | |
| make[5]: Nothing to be done for `install-exec-am'. | |
| make[5]: Nothing to be done for `install-data-am'. | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/tests' | |
| make[4]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib/tests' | |
| make[4]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| make[5]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| test -z "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin" || /bin/mkdir -p "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin" | |
| /usr/bin/install -c io_lib-config '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/bin' | |
| test -z "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man1" || /bin/mkdir -p "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man1" | |
| /usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man1' | |
| test -z "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man3" || /bin/mkdir -p "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man3" | |
| /usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man3' | |
| test -z "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man4" || /bin/mkdir -p "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man4" | |
| /usr/bin/install -c -m 644 man/man4/Read.4 '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/share/man/man4' | |
| test -z "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib" || /bin/mkdir -p "/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib" | |
| /usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/zfio.h '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib' | |
| /usr/bin/install -c -m 644 io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib_config.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h '/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib' | |
| make[5]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| make[4]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| make[3]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/staden-io_lib && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/src/libstadenio-stamp/libstadenio-install | |
| [ 65%] Completed 'libstadenio' | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E make_directory /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/CMakeFiles/libstadenio-complete | |
| /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E touch /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/libstadenio-prefix/src/libstadenio-stamp/libstadenio-done | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 65%] Built target libstadenio | |
| make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CMakeFiles/salmon_core.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target salmon_core | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 66%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/LibraryFormat.cpp | |
| [ 67%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/GenomicFeature.cpp | |
| [ 68%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/VersionChecker.cpp | |
| [ 69%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:12: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:12, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:13: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:18:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp: In constructor 'ReadExperiment::ReadExperiment(std::vector<ReadLibrary>&, const boost::filesystem::path&, SalmonOpts&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:448:39: warning: 'ReadExperiment::totalAssignedFragments_' will be initialized after [-Wreorder] | |
| uint64_t totalAssignedFragments_{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:439:52: warning: 'std::vector<FragmentStartPositionDistribution> ReadExperiment::fragStartDists_' [-Wreorder] | |
| std::vector<FragmentStartPositionDistribution> fragStartDists_; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:18:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:44:5: warning: when initialized here [-Wreorder] | |
| ReadExperiment(std::vector<ReadLibrary>& readLibraries, | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:18:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:129:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < compLen; ++i) { seq[i] = nucTab[rseq[i]]; } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp: In function 'TranscriptGeneMap salmon::utils::transcriptGeneMapFromGTF(const string&, std::__cxx11::string)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:786:12: warning: unused variable 'transcriptCounter' [-Wunused-variable] | |
| size_t transcriptCounter = 0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp: In instantiation of 'void salmon::utils::normalizeAlphas(const SalmonOpts&, AlnLibT&) [with AlnLibT = ReadExperiment]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:1159:54: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:355:10: warning: unused variable 'v' [-Wunused-variable] | |
| double v = transcript.projectedCounts / numMappedReads; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:297:22: warning: unused variable 'logNumFragments' [-Wunused-variable] | |
| const double logNumFragments = std::log(static_cast<double>(numMappedReads)); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:353:9: warning: unused variable 'invNFracTotal' [-Wunused-variable] | |
| double invNFracTotal = 1.0 / nFracDenom; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp: In instantiation of 'void salmon::utils::normalizeAlphas(const SalmonOpts&, AlnLibT&) [with AlnLibT = AlignmentLibrary<UnpairedRead>]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:1163:70: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:355:10: warning: unused variable 'v' [-Wunused-variable] | |
| double v = transcript.projectedCounts / numMappedReads; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:297:22: warning: unused variable 'logNumFragments' [-Wunused-variable] | |
| const double logNumFragments = std::log(static_cast<double>(numMappedReads)); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:353:9: warning: unused variable 'invNFracTotal' [-Wunused-variable] | |
| double invNFracTotal = 1.0 / nFracDenom; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp: In instantiation of 'void salmon::utils::normalizeAlphas(const SalmonOpts&, AlnLibT&) [with AlnLibT = AlignmentLibrary<ReadPair>]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:1166:66: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:355:10: warning: unused variable 'v' [-Wunused-variable] | |
| double v = transcript.projectedCounts / numMappedReads; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:297:22: warning: unused variable 'logNumFragments' [-Wunused-variable] | |
| const double logNumFragments = std::log(static_cast<double>(numMappedReads)); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:353:9: warning: unused variable 'invNFracTotal' [-Wunused-variable] | |
| double invNFracTotal = 1.0 / nFracDenom; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:5, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonUtils.cpp:12: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 70%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonStringUtils.cpp | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonStringUtils.cpp: In function 'uint8_t* salmon::stringtools::encodeSequenceInSAM(const char*, size_t)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonStringUtils.cpp:12:51: warning: array subscript has type 'char' [-Wchar-subscripts] | |
| target[byte] |= charToSamEncode[src[i]]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonStringUtils.cpp:14:52: warning: array subscript has type 'char' [-Wchar-subscripts] | |
| target[byte] |= (charToSamEncode[src[i]] << 4); | |
| ^ | |
| At global scope: | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 72%] Building CXX object src/CMakeFiles/salmon_core.dir/ComputeBiasFeatures.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/ComputeBiasFeatures.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp: In instantiation of 'computeBiasFeaturesHelper(ParserT&, tbb::concurrent_bounded_queue<Sailfish::TranscriptFeatures>&, size_t&, size_t)::<lambda()> [with ParserT = jellyfish::whole_sequence_parser<jellyfish::stream_manager<char**> >]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp:69:87: required from 'struct computeBiasFeaturesHelper(ParserT&, tbb::concurrent_bounded_queue<Sailfish::TranscriptFeatures>&, size_t&, size_t) [with ParserT = jellyfish::whole_sequence_parser<jellyfish::stream_manager<char**> >; size_t = long unsigned int]::<lambda()>' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp:68:26: required from 'bool computeBiasFeaturesHelper(ParserT&, tbb::concurrent_bounded_queue<Sailfish::TranscriptFeatures>&, size_t&, size_t) [with ParserT = jellyfish::whole_sequence_parser<jellyfish::stream_manager<char**> >; size_t = long unsigned int]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp:218:58: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp:93:43: warning: unused variable 'end' [-Wunused-variable] | |
| const char* const end = start + readLen; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp:71:31: warning: variable 'numKmers' set but not used [-Wunused-but-set-variable] | |
| size_t cmlen, numKmers; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp: In instantiation of 'bool computeBiasFeaturesHelper(ParserT&, tbb::concurrent_bounded_queue<Sailfish::TranscriptFeatures>&, size_t&, size_t) [with ParserT = jellyfish::whole_sequence_parser<jellyfish::stream_manager<char**> >; size_t = long unsigned int]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp:218:58: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ComputeBiasFeatures.cpp:67:15: warning: unused variable 'i' [-Wunused-variable] | |
| for (auto i : boost::irange(size_t{0}, numActors)) { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 73%] Building CXX object src/CMakeFiles/salmon_core.dir/PerformBiasCorrection.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/PerformBiasCorrection.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:932:28: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder2nd<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:936:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder1st<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::MatrixBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator==(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::not_equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator!=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:38: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_classes.h:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/ios_base.h:41, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ios:42, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/ostream:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iostream:39, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:39:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/PCA.hpp: In member function 'void PCA::performDecomposition(bool)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/PCA.hpp:30:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < dat_.cols(); ++i) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/PCA.hpp:31:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t j = 0; j < dat_.rows(); ++j) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/PCA.hpp:48:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < dat_.cols(); ++i) { | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/Tree.h:19:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/TreeRegressor.h:15, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:15, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestRegressor.h:15, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:42: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h: In constructor 'FeatureData::FeatureData(uint, uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:85:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nSamples; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:87:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int j=0; j<nFeaures; j++) | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:94:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nFeaures; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:104:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nSamples; i++) | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h: In destructor 'FeatureData::~FeatureData()': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:121:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nSamples; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:126:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nFeatures; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h: In member function 'void FeatureData::reset()': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:142:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nSamples; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h: In member function 'void FeatureData::sort()': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:163:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nSamples; i++) | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:167:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int f=0; f<nFeatures; f++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:169:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nSamples; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:178:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nSamples; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:185:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i=0; i<nSamples; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h: In member function 'uint_vec FeatureData::getNodeSamples(uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/FeatureData.h:203:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (sample_in_node[k]==i) { | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/TreeRegressor.h:15:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:15, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestRegressor.h:15, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:42: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/Tree.h: In constructor 'Tree::Tree(int, uint, uint, uint, uint, uint, uint, uint, uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/Tree.h:131:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (n_threads>max_thread) { | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/TreeRegressor.h:15:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:15, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestRegressor.h:15, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:42: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/Tree.h: In member function 'int Tree::build(REAL**, REAL*, uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/Tree.h:325:88: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (nodes[work_node_id]->nSamples<2*min_sample_leaf || nodes_deep[work_node_id]==max_depth || numNodes>=max_nNodes-2) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/Tree.h: In member function 'bool Tree::find_best_split(uint, REAL**, REAL*, uint*, uint, uint, uint, uint&, REAL&, REAL&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/Tree.h:401:14: warning: variable 'node_nSamples' set but not used [-Wunused-but-set-variable] | |
| uint i,j,node_nSamples,f,count; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/Tree.h: In function 'void find_best_split_range(bool*, Criterion*, REAL**, REAL*, split_args, uint&, REAL&, REAL&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/Tree.h:665:10: warning: unused variable 'ini_error' [-Wunused-variable] | |
| REAL ini_error=min_error; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestRegressor.h:15:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:42: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h: In constructor 'BaseForest::BaseForest(int, uint, uint, uint, uint, REAL, uint, bool, bool, bool, uint, uint, bool)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:88:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (n_jobs>max_thread) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h: In function 'void RF_build_trees_range(REAL**, REAL*, uint, BaseForest*, std::pair<unsigned int, unsigned int>, uint*, REAL*, REAL*)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:353:10: warning: unused variable 'random_seed' [-Wunused-variable] | |
| uint random_seed=forest->random_seed; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMRegressor.h:15:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:44: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseGBM.h: In constructor 'BaseGBM::BaseGBM(int, uint, uint, uint, uint, REAL, REAL, REAL, bool, bool, uint, uint, int)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseGBM.h:114:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (n_jobs>max_thread) { | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMRegressor.h:15:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:44: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseGBM.h: In member function 'bool BaseGBM::load_model(const char*)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseGBM.h:266:112: warning: writing into constant object (argument 3) [-Wformat=] | |
| fscanf(stderr, "Error: Cannot open file %s for load GBM model.Please check your model file.\n",filename); | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:45:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h: In member function 'virtual int GBMClassifier::build(REAL**, REAL*, uint, REAL**, REAL*, uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h:93:84: warning: unused variable 'train_score' [-Wunused-variable] | |
| REAL* y_pred,*y_pred_label,*val_pred,*val_pred_stage,*val_pred_label,*residual,train_score,oob_score; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:46:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/ReadData.h: In function 'bool readData(Data&, const char*, const char*)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/ReadData.h:112:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (uint i=0; i<n_samples; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp: In function 'int performBiasCorrectionSalmon(boost::filesystem::path, boost::filesystem::path, boost::filesystem::path, std::size_t)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:337:16: warning: unused variable 'length' [-Wunused-variable] | |
| auto length = r.length; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:216:16: warning: unused variable 'linearIndex' [-Wunused-variable] | |
| size_t linearIndex{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:251:16: warning: unused variable 'minDepth' [-Wunused-variable] | |
| size_t minDepth = 5; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:322:15: warning: variable 'mpzero' set but not used [-Wunused-but-set-variable] | |
| mpdec mpzero = 0; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:43:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestClassifier.h: In member function 'void RandomForestClassifier::score2label(REAL*, REAL*, uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestClassifier.h:197:43: warning: 'idx' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| pred_label[i]=original_classes[idx]; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:45:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h: In member function 'void GBMClassifier::score2label(REAL*, REAL*, uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h:306:48: warning: 'label_idx' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| label[i]=original_classes[label_idx]; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:43:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestClassifier.h: In member function 'virtual int RandomForestClassifier::build(REAL**, REAL*, uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestClassifier.h:134:28: warning: 'oob_label_prediction' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| oob_scores=Accuracy(original_y, oob_label_prediction, n_samples); | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestRegressor.h:15:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:42: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h: In function 'void RF_build_trees_range(REAL**, REAL*, uint, BaseForest*, std::pair<unsigned int, unsigned int>, uint*, REAL*, REAL*)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:446:49: warning: 'importance_tmp' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| importances[j]+=importance_tmp[j]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:434:27: warning: 'mask' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| if (mask[j]) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:439:84: warning: 'oob_prediction_tmp' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| oob_prediction[j*n_classes+k]+=oob_prediction_tmp[j*n_classes+k]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:401:32: warning: 'sub_y' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| sub_y[j]=y[idx]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/BaseForest.h:400:32: warning: 'sub_X' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| sub_X[j]=X[idx]; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:42:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestRegressor.h: In function 'void RFG_build_trees_range(REAL**, REAL*, uint, BaseForest*, uint, uint, uint*, REAL*, REAL*)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestRegressor.h:182:31: warning: 'importance_tmp' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| REAL *oob_prediction_tmp,*importance_tmp; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestRegressor.h:215:32: warning: 'sub_y' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| sub_y[j]=y[idx]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/RandomForestRegressor.h:214:32: warning: 'sub_X' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| sub_X[j]=X[idx]; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:44:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMRegressor.h: In member function 'virtual int GBMRegressor::build(REAL**, REAL*, uint, REAL**, REAL*, uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMRegressor.h:55:29: warning: 'val_pred_stage' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| REAL* y_pred,*val_pred,*val_pred_stage,*residual,train_score,oob_score,valid_score; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMRegressor.h:113:39: warning: 'sub_y' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| sub_y[j]=residual[idx]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMRegressor.h:112:32: warning: 'sub_X' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| sub_X[j]=X[idx]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMRegressor.h:111:35: warning: 'sample_index' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| idx=sample_index[k]; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/PerformBiasCorrection.cpp:45:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h: In member function 'virtual int GBMClassifier::build(REAL**, REAL*, uint, REAL**, REAL*, uint)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h:251:24: warning: 'val_pred_label' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| fprintf(stderr, ",validation Acc=%f",Accuracy(val_y, val_pred_label, n_val_samples)); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h:228:84: warning: 'val_pred_stage' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| val_pred[offset+j]+=this->learning_rate*val_pred_stage[offset+j]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h:228:85: warning: 'val_pred' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| val_pred[offset+j]+=this->learning_rate*val_pred_stage[offset+j]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h:195:94: warning: 'zero_one_y' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| loss->compute_residual(kth_residual, zero_one_y, y_pred, n_samples, n_classes, k); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h:200:34: warning: 'sub_y' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| sub_y[count++]=kth_residual[idx]; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h:92:12: warning: 'sub_X' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| REAL** sub_X,*sub_y,*y,*zero_one_y; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/tensemble/GBMClassifier.h:199:39: warning: 'sample_index' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| idx=sample_index[j]; | |
| ^ | |
| At global scope: | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 74%] Building CXX object src/CMakeFiles/salmon_core.dir/cokus.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/cokus.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/cokus.cpp | |
| [ 75%] Building CXX object src/CMakeFiles/salmon_core.dir/merge_files.cc.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/merge_files.cc.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/merge_files.cc | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/merge_files.cc:36:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] | |
| typedef std::auto_ptr<binary_reader> binary_reader_ptr; | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_conv.h:41:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/locale:43, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iomanip:43, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3/jellyfish/err.hpp:21, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/merge_files.hpp:21, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/merge_files.cc:17: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/unique_ptr.h:49:28: note: declared here | |
| template<typename> class auto_ptr; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/merge_files.cc:37:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] | |
| typedef std::auto_ptr<text_reader> text_reader_ptr; | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_conv.h:41:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/locale:43, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iomanip:43, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3/jellyfish/err.hpp:21, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/merge_files.hpp:21, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/merge_files.cc:17: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/unique_ptr.h:49:28: note: declared here | |
| template<typename> class auto_ptr; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/merge_files.cc:48:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] | |
| typedef std::auto_ptr<RectangularBinaryMatrix> matrix_ptr; | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/locale_conv.h:41:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/locale:43, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/iomanip:43, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3/jellyfish/err.hpp:21, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/merge_files.hpp:21, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/merge_files.cc:17: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/unique_ptr.h:49:28: note: declared here | |
| template<typename> class auto_ptr; | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 76%] Building CXX object src/CMakeFiles/salmon_core.dir/format.cc.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon_core.dir/format.cc.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/format.cc | |
| [ 77%] Linking CXX static library libsalmon_core.a | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 | |
| /usr/bin/ar qc libsalmon_core.a CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/ComputeBiasFeatures.cpp.o CMakeFiles/salmon_core.dir/PerformBiasCorrection.cpp.o CMakeFiles/salmon_core.dir/cokus.cpp.o CMakeFiles/salmon_core.dir/merge_files.cc.o CMakeFiles/salmon_core.dir/format.cc.o | |
| /usr/bin/ranlib libsalmon_core.a | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 77%] Built target salmon_core | |
| make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/depend | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2 /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CMakeFiles/salmon.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target salmon | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build | |
| make[2]: Entering directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| [ 79%] Building C object src/CMakeFiles/salmon.dir/QSufSort.c.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/gcc-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -Os -w -pipe -march=core2 -DNDEBUG -o CMakeFiles/salmon.dir/QSufSort.c.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/QSufSort.c | |
| [ 80%] Building C object src/CMakeFiles/salmon.dir/is.c.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/gcc-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -Os -w -pipe -march=core2 -DNDEBUG -o CMakeFiles/salmon.dir/is.c.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/is.c | |
| [ 81%] Building C object src/CMakeFiles/salmon.dir/bwt_gen.c.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/gcc-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -Os -w -pipe -march=core2 -DNDEBUG -o CMakeFiles/salmon.dir/bwt_gen.c.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/bwt_gen.c | |
| [ 82%] Building C object src/CMakeFiles/salmon.dir/bwtindex.c.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/gcc-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -Os -w -pipe -march=core2 -DNDEBUG -o CMakeFiles/salmon.dir/bwtindex.c.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/bwtindex.c | |
| [ 83%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:932:28: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder2nd<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:936:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder1st<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::MatrixBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator==(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::not_equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator!=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:19: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:12, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:9, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:12, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:9, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(std::size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:9:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp: In constructor 'ReadExperiment::ReadExperiment(std::vector<ReadLibrary>&, const boost::filesystem::path&, SalmonOpts&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:448:39: warning: 'ReadExperiment::totalAssignedFragments_' will be initialized after [-Wreorder] | |
| uint64_t totalAssignedFragments_{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:439:52: warning: 'std::vector<FragmentStartPositionDistribution> ReadExperiment::fragStartDists_' [-Wreorder] | |
| std::vector<FragmentStartPositionDistribution> fragStartDists_; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:9:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:44:5: warning: when initialized here [-Wreorder] | |
| ReadExperiment(std::vector<ReadLibrary>& readLibraries, | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:9:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:129:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < compLen; ++i) { seq[i] = nucTab[rseq[i]]; } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp: In lambda function: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:164:21: warning: unused variable 'priorNorm' [-Wunused-variable] | |
| double priorNorm = prior * totLen; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp: In function 'std::size_t markDegenerateClasses(std::vector<std::pair<const TranscriptGroup, TGValue> >&, CollapsedEMOptimizer::VecType&, std::shared_ptr<spdlog::logger>, bool)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:232:12: warning: unused variable 'idx' [-Wunused-variable] | |
| size_t idx{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp: In instantiation of 'bool CollapsedEMOptimizer::optimize(ExpT&, SalmonOpts&, double, uint32_t) [with ExpT = ReadExperiment; uint32_t = unsigned int]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:430:25: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:313:12: warning: unused variable 'totalNumFrags' [-Wunused-variable] | |
| double totalNumFrags{static_cast<double>(readExp.numMappedReads())}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp: In instantiation of 'bool CollapsedEMOptimizer::optimize(ExpT&, SalmonOpts&, double, uint32_t) [with ExpT = AlignmentLibrary<UnpairedRead>; uint32_t = unsigned int]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:437:25: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:313:12: warning: unused variable 'totalNumFrags' [-Wunused-variable] | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp: In instantiation of 'bool CollapsedEMOptimizer::optimize(ExpT&, SalmonOpts&, double, uint32_t) [with ExpT = AlignmentLibrary<ReadPair>; uint32_t = unsigned int]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:445:25: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:313:12: warning: unused variable 'totalNumFrags' [-Wunused-variable] | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:5, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:12, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:9, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedEMOptimizer.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 84%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:932:28: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder2nd<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:936:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder1st<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::MatrixBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator==(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::not_equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator!=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:21: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/stdexcept:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/array:38, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/tuple:39, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:41, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:2: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:24: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:24:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(std::size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:30:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp: In constructor 'ReadExperiment::ReadExperiment(std::vector<ReadLibrary>&, const boost::filesystem::path&, SalmonOpts&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:448:39: warning: 'ReadExperiment::totalAssignedFragments_' will be initialized after [-Wreorder] | |
| uint64_t totalAssignedFragments_{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:439:52: warning: 'std::vector<FragmentStartPositionDistribution> ReadExperiment::fragStartDists_' [-Wreorder] | |
| std::vector<FragmentStartPositionDistribution> fragStartDists_; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:30:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:44:5: warning: when initialized here [-Wreorder] | |
| ReadExperiment(std::vector<ReadLibrary>& readLibraries, | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:30:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:129:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < compLen; ++i) { seq[i] = nucTab[rseq[i]]; } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:31:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/MultinomialSampler.hpp: In member function 'void MultinomialSampler::operator()(std::vector<int>::iterator, uint32_t, uint32_t, std::vector<double>::iterator, bool)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/MultinomialSampler.hpp:29:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (i = 1; i <= k; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/MultinomialSampler.hpp:35:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (j = 0; j < n; j++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/MultinomialSampler.hpp:38:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (i = 0; i < k; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp: In function 'void sampleRound_(std::vector<std::pair<const TranscriptGroup, TGValue> >&, std::vector<int>&, std::vector<double>&, double, std::vector<int>&, MultinomialSampler&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:119:18: warning: unused variable 'classCount' [-Wunused-variable] | |
| uint64_t classCount = eqClass.second.count; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:5, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/CollapsedGibbsSampler.cpp:24: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 86%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/Salmon.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/Salmon.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SailfishUtils.hpp:37:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/Salmon.cpp:44: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/Salmon.cpp: In function 'int main(int, char**)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/Salmon.cpp:210:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < subCommandArgc; ++i) { | |
| ^ | |
| At global scope: | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 87%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/BuildSalmonIndex.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/BuildSalmonIndex.cpp:44: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/BuildSalmonIndex.cpp:44:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/BuildSalmonIndex.cpp: In function 'int salmonIndex(int, char**)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/BuildSalmonIndex.cpp:213:16: warning: unused variable 'max_q_size' [-Wunused-variable] | |
| size_t max_q_size = 2097152; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:5, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/BuildSalmonIndex.cpp:44: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 88%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:96: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:96: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:109:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp: In constructor 'ReadExperiment::ReadExperiment(std::vector<ReadLibrary>&, const boost::filesystem::path&, SalmonOpts&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:448:39: warning: 'ReadExperiment::totalAssignedFragments_' will be initialized after [-Wreorder] | |
| uint64_t totalAssignedFragments_{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:439:52: warning: 'std::vector<FragmentStartPositionDistribution> ReadExperiment::fragStartDists_' [-Wreorder] | |
| std::vector<FragmentStartPositionDistribution> fragStartDists_; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:109:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:44:5: warning: when initialized here [-Wreorder] | |
| ReadExperiment(std::vector<ReadLibrary>& readLibraries, | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:109:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:129:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < compLen; ++i) { seq[i] = nucTab[rseq[i]]; } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:932:28: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder2nd<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:936:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder1st<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::MatrixBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator==(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::not_equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator!=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:112: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:23: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In function 'void mem_collect_intv(const SalmonOpts&, const mem_opt_t*, const bwt_t*, int, const uint8_t*, smem_aux_t*)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:168:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (i = 0; i < a->mem1.n; ++i) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:181:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (end - start < split_len || p->x[2] > opt->split_width) continue; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:183:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (i = 0; i < a->mem1.n; ++i) | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:184:71: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if ((uint32_t)a->mem1.a[i].info - (a->mem1.a[i].info>>32) >= opt->min_seed_len) | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:198:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (i = 0; i < a->mem1.n; ++i) | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In constructor 'SMEMAlignment::SMEMAlignment()': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:273:18: warning: 'SMEMAlignment::fragLength_' will be initialized after [-Wreorder] | |
| uint32_t fragLength_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:254:16: warning: 'double SMEMAlignment::logProb' [-Wreorder] | |
| double logProb; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:224:9: warning: when initialized here [-Wreorder] | |
| SMEMAlignment() : | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In constructor 'SMEMAlignment::SMEMAlignment(TranscriptID, LibraryFormat, double, int32_t, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:273:18: warning: 'SMEMAlignment::fragLength_' will be initialized after [-Wreorder] | |
| uint32_t fragLength_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:254:16: warning: 'double SMEMAlignment::logProb' [-Wreorder] | |
| double logProb; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:233:9: warning: when initialized here [-Wreorder] | |
| SMEMAlignment(TranscriptID transcriptIDIn, LibraryFormat format, | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In function 'void processMiniBatch(ReadExperiment&, ForgettingMassCalculator&, uint64_t, ReadLibrary&, const SalmonOpts&, std::vector<AlignmentGroup<SMEMAlignment>*>&, std::vector<Transcript>&, ClusterForest&, FragmentLengthDistribution&, std::atomic<long unsigned int>&, std::default_random_engine&, bool, bool&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:454:28: warning: unused variable 'errLike' [-Wunused-variable] | |
| double errLike = salmon::math::LOG_1; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:636:20: warning: unused variable 'avgBias' [-Wunused-variable] | |
| double avgBias = std::exp(avgLogBias); | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:24:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:96: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonMath.hpp:12:26: warning: unused variable 'salmon::math::LOG_ONEHALF' [-Wunused-variable] | |
| constexpr double LOG_ONEHALF = -0.69314718055994530941; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:309:12: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts{transcripts.size()}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:311:12: warning: unused variable 'priorNumAssignedFragments' [-Wunused-variable] | |
| size_t priorNumAssignedFragments{numAssignedFragments}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:392:9: warning: unused variable 'i' [-Wunused-variable] | |
| int i{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:657:16: warning: unused variable 'individualTotal' [-Wunused-variable] | |
| double individualTotal = LOG_0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In member function 'bool TranscriptHitList::computeBestLoc2_(std::vector<KmerVote>&, uint32_t, int32_t&, uint32_t&, double&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:842:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| uint32_t leftmost = (sVotes.front().votePos > maxGap) ? (sVotes.front().votePos - maxGap) : 0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:855:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| while (x < nvotes and sVotes[x].votePos == votePos) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:847:20: warning: unused variable 'kwidth' [-Wunused-variable] | |
| double kwidth = 1.0 / (2.0 * maxGap); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In member function 'uint32_t TranscriptHitList::numSampledHits_(Transcript&, std::__cxx11::string&, int32_t, int32_t, int32_t, bool, uint32_t)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:962:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for ( size_t j = 0; j < readLen; ++j) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:964:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (j == posInRead) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:970:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (j == posInRead + voteLen) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:976:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (j == posInRead ) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:982:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (j == posInRead + voteLen) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1044:131: warning: array subscript has type 'char' [-Wchar-subscripts] | |
| (transcript.charBaseAt(readStart + readLen - readPos, dir) == salmon::stringtools::charCanon[read[readPos]]) : | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1045:131: warning: array subscript has type 'char' [-Wchar-subscripts] | |
| (transcript.charBaseAt(readStart + readPos ) == salmon::stringtools::charCanon[read[readPos]]); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In function 'void processCachedAlignmentsHelper(ReadExperiment&, ReadLibrary&, AlnGroupQueue&, AlnGroupQueue&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::vector<Transcript>&, ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&, const SalmonOpts&, std::mutex&, bool, volatile bool&, bool&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1974:10: warning: variable 'expectedLibType' set but not used [-Wunused-but-set-variable] | |
| auto expectedLibType = rl.format(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In function 'void processReadLibrary(ReadExperiment&, ReadLibrary&, bwaidx_t*, std::vector<Transcript>&, ClusterForest&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, bool, bool&, ForgettingMassCalculator&, FragmentLengthDistribution&, mem_opt_t*, const SalmonOpts&, double, bool, std::mutex&, std::size_t, AlnGroupQueue&, AlnGroupQueue&, volatile bool&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2180:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int i = 0; i < numThreads; ++i) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2234:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int i = 0; i < numThreads; ++i) | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2251:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int i = 0; i < numThreads; ++i) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2301:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int i = 0; i < numThreads; ++i) | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2240:23: warning: unused variable 'readFiles' [-Wunused-variable] | |
| char* readFiles[] = { const_cast<char*>(rl.unmated().front().c_str()) }; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In function 'void quantifyLibrary(ReadExperiment&, bool, mem_opt_t*, SalmonOpts&, double, std::size_t, uint32_t)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2732:18: warning: unused variable 'done' [-Wunused-variable] | |
| bool done = experiment.equivalenceClassBuilder().finish(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2585:10: warning: unused variable 'burnedIn' [-Wunused-variable] | |
| bool burnedIn{false}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2589:12: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts = refs.size(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In function 'int salmonQuantify(int, char**)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:3126:16: warning: unused variable 'tnum' [-Wunused-variable] | |
| size_t tnum{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In instantiation of 'void processReadsMEM(ParserT*, ReadExperiment&, ReadLibrary&, AlnGroupQueue&, AlnGroupQueue&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, bwaidx_t*, std::vector<Transcript>&, ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&, mem_opt_t*, const SalmonOpts&, double, std::mutex&, bool, bool&, volatile bool&) [with ParserT = pair_sequence_parser<char**>; CoverageCalculator = TranscriptHitList; AlnGroupQueue = moodycamel::ConcurrentQueue<AlignmentGroup<SMEMAlignment>*>]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2204:49: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1813:12: warning: unused variable 'count_fwd' [-Wunused-variable] | |
| uint64_t count_fwd = 0, count_bwd = 0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1813:27: warning: unused variable 'count_bwd' [-Wunused-variable] | |
| uint64_t count_fwd = 0, count_bwd = 0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1825:12: warning: unused variable 'leftHitCount' [-Wunused-variable] | |
| uint64_t leftHitCount{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1833:8: warning: variable 'expectedLibType' set but not used [-Wunused-but-set-variable] | |
| auto expectedLibType = rl.format(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In instantiation of 'void processReadsMEM(ParserT*, ReadExperiment&, ReadLibrary&, AlnGroupQueue&, AlnGroupQueue&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, bwaidx_t*, std::vector<Transcript>&, ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&, mem_opt_t*, const SalmonOpts&, double, std::mutex&, bool, bool&, volatile bool&) [with ParserT = jellyfish::whole_sequence_parser<jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const std::__cxx11::basic_string<char>*, std::vector<std::__cxx11::basic_string<char> > > > >; CoverageCalculator = TranscriptHitList; AlnGroupQueue = moodycamel::ConcurrentQueue<AlignmentGroup<SMEMAlignment>*>]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2275:49: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1813:12: warning: unused variable 'count_fwd' [-Wunused-variable] | |
| uint64_t count_fwd = 0, count_bwd = 0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1813:27: warning: unused variable 'count_bwd' [-Wunused-variable] | |
| uint64_t count_fwd = 0, count_bwd = 0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1825:12: warning: unused variable 'leftHitCount' [-Wunused-variable] | |
| uint64_t leftHitCount{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1833:8: warning: variable 'expectedLibType' set but not used [-Wunused-but-set-variable] | |
| auto expectedLibType = rl.format(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In instantiation of 'void getHitsForFragment(std::pair<header_sequence_qual, header_sequence_qual>&, bwaidx_t*, smem_i*, const bwtintv_v*, smem_aux_t*, mem_opt_t*, const SalmonOpts&, double, uint64_t&, AlignmentGroup<SMEMAlignment>&, uint64_t&, std::vector<Transcript>&) [with CoverageCalculator = TranscriptHitList; smem_i = __smem_i; uint64_t = long unsigned int]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1859:47: required from 'void processReadsMEM(ParserT*, ReadExperiment&, ReadLibrary&, AlnGroupQueue&, AlnGroupQueue&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, bwaidx_t*, std::vector<Transcript>&, ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&, mem_opt_t*, const SalmonOpts&, double, std::mutex&, bool, bool&, volatile bool&) [with ParserT = pair_sequence_parser<char**>; CoverageCalculator = TranscriptHitList; AlnGroupQueue = moodycamel::ConcurrentQueue<AlignmentGroup<SMEMAlignment>*>]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2204:49: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1405:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int p = 0; p < readLen; ++p) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1424:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int p = 0; p < readLen; ++p) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1508:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (transcriptID < lastTranscriptId) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1483:14: warning: variable 'foundValidHit' set but not used [-Wunused-but-set-variable] | |
| bool foundValidHit{false}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1603:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (transcriptID < lastTranscriptId) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In instantiation of 'void getHitsForFragment(jellyfish::header_sequence_qual&, bwaidx_t*, smem_i*, const bwtintv_v*, smem_aux_t*, mem_opt_t*, const SalmonOpts&, double, uint64_t&, AlignmentGroup<SMEMAlignment>&, uint64_t&, std::vector<Transcript>&) [with CoverageCalculator = TranscriptHitList; smem_i = __smem_i; uint64_t = long unsigned int]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1859:47: required from 'void processReadsMEM(ParserT*, ReadExperiment&, ReadLibrary&, AlnGroupQueue&, AlnGroupQueue&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, bwaidx_t*, std::vector<Transcript>&, ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&, mem_opt_t*, const SalmonOpts&, double, std::mutex&, bool, bool&, volatile bool&) [with ParserT = jellyfish::whole_sequence_parser<jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const std::__cxx11::basic_string<char>*, std::vector<std::__cxx11::basic_string<char> > > > >; CoverageCalculator = TranscriptHitList; AlnGroupQueue = moodycamel::ConcurrentQueue<AlignmentGroup<SMEMAlignment>*>]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2275:49: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1706:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int p = 0; p < readLen; ++p) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1710:15: warning: unused variable 'readPtr' [-Wunused-variable] | |
| char* readPtr = const_cast<char*>(readStr.c_str()); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1760:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (transcriptID < lastTranscriptId) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1697:14: warning: variable 'readLength' set but not used [-Wunused-but-set-variable] | |
| uint32_t readLength{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp: In instantiation of 'void collectHitsForRead(const bwaidx_t*, const bwtintv_v*, smem_aux_t*, mem_opt_t*, const SalmonOpts&, const uint8_t*, uint32_t, std::unordered_map<long unsigned int, CoverageCalculator>&) [with CoverageCalculator = TranscriptHitList; uint8_t = unsigned char; uint32_t = unsigned int]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1409:27: required from 'void getHitsForFragment(std::pair<header_sequence_qual, header_sequence_qual>&, bwaidx_t*, smem_i*, const bwtintv_v*, smem_aux_t*, mem_opt_t*, const SalmonOpts&, double, uint64_t&, AlignmentGroup<SMEMAlignment>&, uint64_t&, std::vector<Transcript>&) [with CoverageCalculator = TranscriptHitList; smem_i = __smem_i; uint64_t = long unsigned int]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1859:47: required from 'void processReadsMEM(ParserT*, ReadExperiment&, ReadLibrary&, AlnGroupQueue&, AlnGroupQueue&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, bwaidx_t*, std::vector<Transcript>&, ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&, mem_opt_t*, const SalmonOpts&, double, std::mutex&, bool, bool&, volatile bool&) [with ParserT = pair_sequence_parser<char**>; CoverageCalculator = TranscriptHitList; AlnGroupQueue = moodycamel::ConcurrentQueue<AlignmentGroup<SMEMAlignment>*>]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:2204:49: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1154:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i = 0; i < auxHits->mem.n; ++i ) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1163:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| step = p->x[2] > memOptions->max_occ? p->x[2] / memOptions->max_occ : 1; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1165:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (k = count = 0; k < p->x[2] && count < memOptions->max_occ; k += step, ++count) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1234:33: warning: unused variable 'votePos' [-Wunused-variable] | |
| int32_t votePos = static_cast<int32_t>(hitLoc) - queryStart; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1246:33: warning: unused variable 'votePos' [-Wunused-variable] | |
| int32_t votePos = static_cast<int32_t>(hitLoc) - queryStart; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1262:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (std::max(len1, len2) < memOptions->min_seed_len) { continue; } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1278:33: warning: unused variable 'votePos' [-Wunused-variable] | |
| int32_t votePos = static_cast<int32_t>(hitLoc) - (rlen - queryStart); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1286:33: warning: unused variable 'votePos' [-Wunused-variable] | |
| int32_t votePos = static_cast<int32_t>(hitLoc) - (rlen - queryStart); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1166:22: warning: variable 'pos' set but not used [-Wunused-but-set-variable] | |
| bwtint_t pos; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:1168:17: warning: variable 'len' set but not used [-Wunused-but-set-variable] | |
| int len, isRev, isRevStart, isRevEnd, refID, refIDStart, refIDEnd; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:26:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:96: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/LibraryFormat.hpp: In member function 'void ReadExperiment::summarizeLibraryTypeCounts(boost::filesystem::path&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/LibraryFormat.hpp:84:40: warning: 'rs' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| return LibraryFormat(rt, ro, rs); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/LibraryFormat.hpp:40:26: note: 'rs' was declared here | |
| ReadStrandedness rs; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/LibraryFormat.hpp: In function 'bool readAlignmentCache(AlnGroupQueue&, AlnGroupQueue&, uint64_t, volatile bool&, boost::filesystem::path&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/LibraryFormat.hpp:84:40: warning: 'rs' may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| return LibraryFormat(rt, ro, rs); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/LibraryFormat.hpp:40:26: note: 'rs' was declared here | |
| ReadStrandedness rs; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:5, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantify.cpp:96: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 89%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentLengthDistribution.cpp | |
| [ 90%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:10:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/FragmentStartPositionDistribution.hpp: In constructor 'FragmentStartPositionDistribution::FragmentStartPositionDistribution(uint32_t)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/FragmentStartPositionDistribution.hpp:43:10: warning: 'FragmentStartPositionDistribution::numBins_' will be initialized after [-Wreorder] | |
| size_t numBins_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/FragmentStartPositionDistribution.hpp:29:36: warning: 'std::vector<tbb::atomic<double> > FragmentStartPositionDistribution::pmf_' [-Wreorder] | |
| std::vector<tbb::atomic<double>> pmf_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:22:1: warning: when initialized here [-Wreorder] | |
| FragmentStartPositionDistribution::FragmentStartPositionDistribution(uint32_t numBins) | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:31:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (auto i = 1; i <= numBins_; ++i) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp: In member function 'void FragmentStartPositionDistribution::addVal(int32_t, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:55:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (hitPos >= txpLen) return; // hit should happen within the transcript | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:67:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| i < (((long long)hitPos + 1) * numBins_ - 1) / txpLen + 1; i++) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp: In member function 'void FragmentStartPositionDistribution::update()': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:89:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i = 1; i <= numBins_; i++) { | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/include/boost/assert.hpp:58:0, | |
| from /home/linuxbrew/.linuxbrew/include/boost/math/tools/roots.hpp:19, | |
| from /home/linuxbrew/.linuxbrew/include/boost/math/special_functions/detail/igamma_inverse.hpp:16, | |
| from /home/linuxbrew/.linuxbrew/include/boost/math/special_functions/gamma.hpp:2027, | |
| from /home/linuxbrew/.linuxbrew/include/boost/math/special_functions/beta.hpp:15, | |
| from /home/linuxbrew/.linuxbrew/include/boost/math/distributions/binomial.hpp:83, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:17: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp: In member function 'double FragmentStartPositionDistribution::operator()(int32_t, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:103:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| assert(hitPos < txpLen); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:104:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (hitPos >= txpLen) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FragmentStartPositionDistribution.cpp:114:12: warning: unused variable 'a' [-Wunused-variable] | |
| double a = hitPos * (1.0 / txpLen); | |
| ^ | |
| At global scope: | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 91%] Building CXX object src/CMakeFiles/salmon.dir/SequenceBiasModel.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/SequenceBiasModel.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SequenceBiasModel.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SequenceBiasModel.cpp:9: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SequenceBiasModel.cpp:9:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SequenceBiasModel.cpp:7:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SequenceBiasModel.hpp: In constructor 'SequenceBiasModel::SequenceBiasModel(double, uint32_t)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SequenceBiasModel.hpp:89:10: warning: 'SequenceBiasModel::isEnabled_' will be initialized after [-Wreorder] | |
| bool isEnabled_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SequenceBiasModel.hpp:88:14: warning: 'uint32_t SequenceBiasModel::windowSize_' [-Wreorder] | |
| uint32_t windowSize_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SequenceBiasModel.cpp:12:1: warning: when initialized here [-Wreorder] | |
| SequenceBiasModel::SequenceBiasModel(double alpha, uint32_t windowSize) : | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SequenceBiasModel.cpp: In member function 'bool SequenceBiasModel::update(Transcript&, int32_t, bool, double, double, AtomicMatrix<double>&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SequenceBiasModel.cpp:48:26: warning: unused variable 'inc' [-Wunused-variable] | |
| int32_t start, stop, inc; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:5, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SequenceBiasModel.cpp:9: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 93%] Building CXX object src/CMakeFiles/salmon.dir/StadenUtils.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/StadenUtils.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/StadenUtils.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/StadenUtils.hpp:5, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/StadenUtils.cpp:1: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 94%] Building CXX object src/CMakeFiles/salmon.dir/TranscriptGroup.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/TranscriptGroup.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/TranscriptGroup.cpp | |
| [ 95%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/FASTAParser.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FASTAParser.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FASTAParser.cpp:12: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FASTAParser.cpp:12:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:5, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/FASTAParser.cpp:12: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 96%] Building CXX object src/CMakeFiles/salmon.dir/ErrorModel.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/ErrorModel.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ErrorModel.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ErrorModel.cpp:7: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ErrorModel.cpp:7:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ErrorModel.cpp:6:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ErrorModel.hpp: In constructor 'ErrorModel::ErrorModel(double, uint32_t)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ErrorModel.hpp:66:12: warning: 'ErrorModel::maxExpectedLen_' will be initialized after [-Wreorder] | |
| size_t maxExpectedLen_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ErrorModel.hpp:60:39: warning: 'std::vector<AtomicMatrix<double> > ErrorModel::mismatchLeft_' [-Wreorder] | |
| std::vector<AtomicMatrix<double>> mismatchLeft_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ErrorModel.cpp:13:1: warning: when initialized here [-Wreorder] | |
| ErrorModel::ErrorModel(double alpha, uint32_t maxExpectedReadLen) : | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ErrorModel.hpp:10, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/ErrorModel.cpp:6: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/AlignmentModel.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:8: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:8:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp: In member function 'bool AlignmentModel::hasIndel(bam_seq_t*)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:51:18: warning: unused variable 'opLen' [-Wunused-variable] | |
| uint32_t opLen = cigar[cigarIdx] >> BAM_CIGAR_SHIFT; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp: In member function 'double AlignmentModel::logLikelihood(bam_seq_t*, Transcript&, std::vector<AtomicMatrix<double> >&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:268:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (readIdx >= readLen) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:215:10: warning: unused variable 'useQual' [-Wunused-variable] | |
| bool useQual{false}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:240:14: warning: unused variable 'qualStr' [-Wunused-variable] | |
| uint8_t* qualStr = reinterpret_cast<uint8_t*>(bam_qual(read)); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:251:14: warning: unused variable 'cigarIdx' [-Wunused-variable] | |
| uint32_t cigarIdx{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp: In member function 'double AlignmentModel::logLikelihood(const ReadPair&, Transcript&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:349:12: warning: unused variable 'leftLen' [-Wunused-variable] | |
| size_t leftLen = static_cast<size_t>(bam_seq_len(leftRead)); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:350:12: warning: unused variable 'rightLen' [-Wunused-variable] | |
| size_t rightLen = static_cast<size_t>(bam_seq_len(rightRead)); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp: In member function 'double AlignmentModel::logLikelihood(const UnpairedRead&, Transcript&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:373:12: warning: unused variable 'readLen' [-Wunused-variable] | |
| size_t readLen = static_cast<size_t>(bam_seq_len(read)); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp: In member function 'void AlignmentModel::update(bam_seq_t*, Transcript&, double, double, std::vector<AtomicMatrix<double> >&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:446:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (readIdx >= readLen) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:429:18: warning: unused variable 'cigarIdx' [-Wunused-variable] | |
| uint32_t cigarIdx{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:401:10: warning: unused variable 'useQual' [-Wunused-variable] | |
| bool useQual{false}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:419:14: warning: unused variable 'qualStr' [-Wunused-variable] | |
| uint8_t* qualStr = reinterpret_cast<uint8_t*>(bam_qual(read)); | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:5, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/AlignmentModel.cpp:8: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/bin/g++-5 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/cereal/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/jellyfish-2.1.3 -I/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/bwa -I/home/linuxbrew/.linuxbrew/include -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -c /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/SalmonUtils.hpp:27:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:8, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:41: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In copy constructor 'ReadLibrary::ReadLibrary(const ReadLibrary&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:35:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp: In constructor 'ReadLibrary::ReadLibrary(ReadLibrary&&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadLibrary.hpp:48:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < mc; ++i) { libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:7:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:41: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp: In constructor 'Transcript::Transcript(size_t, const char*, uint32_t, double)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:232:12: warning: 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder] | |
| double logPerBasePrior_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:225:12: warning: 'double Transcript::priorMass_' [-Wreorder] | |
| double priorMass_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Transcript.hpp:16:5: warning: when initialized here [-Wreorder] | |
| Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 0.05) : | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:9:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp: In constructor 'ReadExperiment::ReadExperiment(std::vector<ReadLibrary>&, const boost::filesystem::path&, SalmonOpts&)': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:448:39: warning: 'ReadExperiment::totalAssignedFragments_' will be initialized after [-Wreorder] | |
| uint64_t totalAssignedFragments_{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:439:52: warning: 'std::vector<FragmentStartPositionDistribution> ReadExperiment::fragStartDists_' [-Wreorder] | |
| std::vector<FragmentStartPositionDistribution> fragStartDists_; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:9:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:44:5: warning: when initialized here [-Wreorder] | |
| ReadExperiment(std::vector<ReadLibrary>& readLibraries, | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:9:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ReadExperiment.hpp:129:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < compLen; ++i) { seq[i] = nucTab[rseq[i]]; } | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:932:28: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder2nd<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:276:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/Functors.h:936:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| struct functor_traits<std::binder1st<T> > | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/MatrixBase.h:138:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:279, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::MatrixBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:62:32: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >, const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:190:34: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| inline const CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:108:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder1st<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::cwiseEqual(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/MatrixCwiseUnaryOps.h:65:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder1st<std::equal_to<Scalar> >,const Derived> | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:108:11: note: declared here | |
| class binder1st | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator==(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:196:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator==, std::equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::not_equal_to<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator!=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:197:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator!=, std::not_equal_to) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:198:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<, std::less) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::less_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator<=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:199:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator<=, std::less_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:200:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>, std::greater) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/ArrayBase.h:109:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Core:350, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/Dense:1, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/CollapsedEMOptimizer.hpp:13, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:62: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h: In member function 'const Eigen::CwiseUnaryOp<std::binder2nd<std::greater_equal<typename Eigen::internal::traits<T>::Scalar> >, const Derived> Eigen::ArrayBase<Derived>::operator>=(const Scalar&) const': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:192:30: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations] | |
| return CwiseUnaryOp<std::binder2nd<FUNCTOR<Scalar> >, const Derived> \ | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/eigen3/Eigen/src/Core/../plugins/ArrayCwiseUnaryOps.h:201:1: note: in expansion of macro 'EIGEN_MAKE_SCALAR_CWISE_UNARY_OP' | |
| EIGEN_MAKE_SCALAR_CWISE_UNARY_OP(operator>=, std::greater_equal) | |
| ^ | |
| In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_function.h:1128:0, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/string:48, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/random:40, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/stl_algo.h:66, | |
| from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/algorithm:62, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/format.h:37, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:8: | |
| /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/backward/binders.h:143:11: note: declared here | |
| class binder2nd | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:42:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp: In instantiation of 'AlignmentLibrary<FragT>::AlignmentLibrary(std::vector<boost::filesystem::path>&, const boost::filesystem::path&, LibraryFormat, SalmonOpts&) [with FragT = UnpairedRead]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1106:63: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:270:52: warning: 'AlignmentLibrary<UnpairedRead>::fragStartDists_' will be initialized after [-Wreorder] | |
| std::vector<FragmentStartPositionDistribution> fragStartDists_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:257:23: warning: 'SequenceBiasModel AlignmentLibrary<UnpairedRead>::seqBiasModel_' [-Wreorder] | |
| SequenceBiasModel seqBiasModel_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:50:5: warning: when initialized here [-Wreorder] | |
| AlignmentLibrary(std::vector<boost::filesystem::path>& alnFiles, | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:287:29: warning: 'AlignmentLibrary<UnpairedRead>::eqBuilder_' will be initialized after [-Wreorder] | |
| EquivalenceClassBuilder eqBuilder_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:285:12: warning: 'size_t AlignmentLibrary<UnpairedRead>::quantificationPasses_' [-Wreorder] | |
| size_t quantificationPasses_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:50:5: warning: when initialized here [-Wreorder] | |
| AlignmentLibrary(std::vector<boost::filesystem::path>& alnFiles, | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:103:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < header->nref; ++i) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp: In instantiation of 'bool quantifyLibrary(AlignmentLibrary<FragT>&, std::size_t, const SalmonOpts&) [with FragT = UnpairedRead; std::size_t = long unsigned int]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1110:101: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:714:16: warning: unused variable 't' [-Wunused-variable] | |
| size_t t = 0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:756:14: warning: unused variable 'done' [-Wunused-variable] | |
| bool done = alnLib.equivalenceClassBuilder().finish(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:556:12: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts = refs.size(); | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:59:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp: In instantiation of 'bool salmon::sampler::sampleLibrary(AlignmentLibrary<FragT>&, const SalmonOpts&, bool, boost::filesystem::path&, bool) [with FragT = UnpairedRead]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1140:142: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:295:24: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts = refs.size(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:301:24: warning: unused variable 'forgettingFactor' [-Wunused-variable] | |
| double forgettingFactor{0.60}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:453:24: warning: unused variable 't' [-Wunused-variable] | |
| size_t t = 0; | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:42:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp: In instantiation of 'AlignmentLibrary<FragT>::AlignmentLibrary(std::vector<boost::filesystem::path>&, const boost::filesystem::path&, LibraryFormat, SalmonOpts&) [with FragT = ReadPair]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1152:59: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:270:52: warning: 'AlignmentLibrary<ReadPair>::fragStartDists_' will be initialized after [-Wreorder] | |
| std::vector<FragmentStartPositionDistribution> fragStartDists_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:257:23: warning: 'SequenceBiasModel AlignmentLibrary<ReadPair>::seqBiasModel_' [-Wreorder] | |
| SequenceBiasModel seqBiasModel_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:50:5: warning: when initialized here [-Wreorder] | |
| AlignmentLibrary(std::vector<boost::filesystem::path>& alnFiles, | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:287:29: warning: 'AlignmentLibrary<ReadPair>::eqBuilder_' will be initialized after [-Wreorder] | |
| EquivalenceClassBuilder eqBuilder_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:285:12: warning: 'size_t AlignmentLibrary<ReadPair>::quantificationPasses_' [-Wreorder] | |
| size_t quantificationPasses_; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:50:5: warning: when initialized here [-Wreorder] | |
| AlignmentLibrary(std::vector<boost::filesystem::path>& alnFiles, | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/AlignmentLibrary.hpp:103:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (size_t i = 0; i < header->nref; ++i) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp: In instantiation of 'bool quantifyLibrary(AlignmentLibrary<FragT>&, std::size_t, const SalmonOpts&) [with FragT = ReadPair; std::size_t = long unsigned int]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1156:97: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:714:16: warning: unused variable 't' [-Wunused-variable] | |
| size_t t = 0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:756:14: warning: unused variable 'done' [-Wunused-variable] | |
| bool done = alnLib.equivalenceClassBuilder().finish(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:556:12: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts = refs.size(); | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:59:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp: In instantiation of 'bool salmon::sampler::sampleLibrary(AlignmentLibrary<FragT>&, const SalmonOpts&, bool, boost::filesystem::path&, bool) [with FragT = ReadPair]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1196:138: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:295:24: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts = refs.size(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:301:24: warning: unused variable 'forgettingFactor' [-Wunused-variable] | |
| double forgettingFactor{0.60}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:453:24: warning: unused variable 't' [-Wunused-variable] | |
| size_t t = 0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp: In instantiation of 'void processMiniBatch(AlignmentLibrary<FragT>&, ForgettingMassCalculator&, uint64_t, MiniBatchQueue<AlignmentGroup<FragT*> >&, MiniBatchQueue<AlignmentGroup<FragT*> >*, std::condition_variable&, std::mutex&, volatile bool&, std::atomic<long unsigned int>&, const SalmonOpts&, bool&, bool, std::atomic<long unsigned int>&) [with FragT = UnpairedRead; uint64_t = long unsigned int; MiniBatchQueue<AlignmentGroup<FragT*> > = tbb::strict_ppl::concurrent_queue<MiniBatchInfo<AlignmentGroup<UnpairedRead*> >*, tbb::cache_aligned_allocator<MiniBatchInfo<AlignmentGroup<UnpairedRead*> >*> >]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:641:13: required from 'bool quantifyLibrary(AlignmentLibrary<FragT>&, std::size_t, const SalmonOpts&) [with FragT = UnpairedRead; std::size_t = long unsigned int]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1110:101: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:222:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (transcriptID < 0 or transcriptID >= refs.size()) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:305:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| } else if (aln->isRight() and aln->right() < fragLengthDist.maxVal()) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:273:24: warning: unused variable 'currentCumulativeMass' [-Wunused-variable] | |
| double currentCumulativeMass = fmCalc.cumulativeLogMassAt(currentMinibatchTimestep); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:476:20: warning: unused variable 'individualTotal' [-Wunused-variable] | |
| double individualTotal = LOG_0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:176:18: warning: unused variable 'zeroProbFrags' [-Wunused-variable] | |
| uint32_t zeroProbFrags{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:180:25: warning: unused variable 'numTries' [-Wunused-variable] | |
| constexpr uint32_t numTries = 100; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:161:10: warning: unused variable 'useFragLengthDist' [-Wunused-variable] | |
| bool useFragLengthDist{!salmonOpts.noFragLengthDist}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:164:12: warning: unused variable 'startingCumulativeMass' [-Wunused-variable] | |
| double startingCumulativeMass = fmCalc.cumulativeLogMassAt(firstTimestepOfRound); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:173:12: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts = refs.size(); | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:59:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp: In instantiation of 'void salmon::sampler::sampleMiniBatch(AlignmentLibrary<FragT>&, salmon::sampler::MiniBatchQueue<AlignmentGroup<FragT*> >&, std::condition_variable&, std::mutex&, volatile bool&, std::atomic<long unsigned int>&, const SalmonOpts&, bool&, std::atomic<long unsigned int>&, salmon::sampler::OutputQueue<FragT>&) [with FragT = UnpairedRead; salmon::sampler::MiniBatchQueue<AlignmentGroup<FragT*> > = tbb::strict_ppl::concurrent_queue<MiniBatchInfo<AlignmentGroup<UnpairedRead*> >*, tbb::cache_aligned_allocator<MiniBatchInfo<AlignmentGroup<UnpairedRead*> >*> >; salmon::sampler::OutputQueue<FragT> = tbb::concurrent_bounded_queue<UnpairedRead*, tbb::cache_aligned_allocator<UnpairedRead*> >]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:343:21: required from 'bool salmon::sampler::sampleLibrary(AlignmentLibrary<FragT>&, const SalmonOpts&, bool, boost::filesystem::path&, bool) [with FragT = UnpairedRead]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1140:142: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:143:70: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (transcriptID < 0 or transcriptID >= refs.size()) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:171:88: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| } else if (aln->isRight() and aln->right() < fragLengthDist.maxVal()) { | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:59:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:104:23: warning: unused variable 'clusterForest' [-Wunused-variable] | |
| auto& clusterForest = alnLib.clusterForest(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:117:24: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts = refs.size(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp: In instantiation of 'void processMiniBatch(AlignmentLibrary<FragT>&, ForgettingMassCalculator&, uint64_t, MiniBatchQueue<AlignmentGroup<FragT*> >&, MiniBatchQueue<AlignmentGroup<FragT*> >*, std::condition_variable&, std::mutex&, volatile bool&, std::atomic<long unsigned int>&, const SalmonOpts&, bool&, bool, std::atomic<long unsigned int>&) [with FragT = ReadPair; uint64_t = long unsigned int; MiniBatchQueue<AlignmentGroup<FragT*> > = tbb::strict_ppl::concurrent_queue<MiniBatchInfo<AlignmentGroup<ReadPair*> >*, tbb::cache_aligned_allocator<MiniBatchInfo<AlignmentGroup<ReadPair*> >*> >]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:641:13: required from 'bool quantifyLibrary(AlignmentLibrary<FragT>&, std::size_t, const SalmonOpts&) [with FragT = ReadPair; std::size_t = long unsigned int]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1156:97: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:222:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (transcriptID < 0 or transcriptID >= refs.size()) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:305:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| } else if (aln->isRight() and aln->right() < fragLengthDist.maxVal()) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:273:24: warning: unused variable 'currentCumulativeMass' [-Wunused-variable] | |
| double currentCumulativeMass = fmCalc.cumulativeLogMassAt(currentMinibatchTimestep); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:476:20: warning: unused variable 'individualTotal' [-Wunused-variable] | |
| double individualTotal = LOG_0; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:176:18: warning: unused variable 'zeroProbFrags' [-Wunused-variable] | |
| uint32_t zeroProbFrags{0}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:180:25: warning: unused variable 'numTries' [-Wunused-variable] | |
| constexpr uint32_t numTries = 100; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:161:10: warning: unused variable 'useFragLengthDist' [-Wunused-variable] | |
| bool useFragLengthDist{!salmonOpts.noFragLengthDist}; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:164:12: warning: unused variable 'startingCumulativeMass' [-Wunused-variable] | |
| double startingCumulativeMass = fmCalc.cumulativeLogMassAt(firstTimestepOfRound); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:173:12: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts = refs.size(); | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:59:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp: In instantiation of 'void salmon::sampler::sampleMiniBatch(AlignmentLibrary<FragT>&, salmon::sampler::MiniBatchQueue<AlignmentGroup<FragT*> >&, std::condition_variable&, std::mutex&, volatile bool&, std::atomic<long unsigned int>&, const SalmonOpts&, bool&, std::atomic<long unsigned int>&, salmon::sampler::OutputQueue<FragT>&) [with FragT = ReadPair; salmon::sampler::MiniBatchQueue<AlignmentGroup<FragT*> > = tbb::strict_ppl::concurrent_queue<MiniBatchInfo<AlignmentGroup<ReadPair*> >*, tbb::cache_aligned_allocator<MiniBatchInfo<AlignmentGroup<ReadPair*> >*> >; salmon::sampler::OutputQueue<FragT> = tbb::concurrent_bounded_queue<ReadPair*, tbb::cache_aligned_allocator<ReadPair*> >]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:343:21: required from 'bool salmon::sampler::sampleLibrary(AlignmentLibrary<FragT>&, const SalmonOpts&, bool, boost::filesystem::path&, bool) [with FragT = ReadPair]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1196:138: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:143:70: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (transcriptID < 0 or transcriptID >= refs.size()) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:171:88: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| } else if (aln->isRight() and aln->right() < fragLengthDist.maxVal()) { | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:59:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:104:23: warning: unused variable 'clusterForest' [-Wunused-variable] | |
| auto& clusterForest = alnLib.clusterForest(); | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/Sampler.hpp:117:24: warning: unused variable 'numTranscripts' [-Wunused-variable] | |
| size_t numTranscripts = refs.size(); | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:41:0: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp: In instantiation of 'void ClusterForest::mergeClusters(typename std::vector<FragT*>::iterator, typename std::vector<FragT*>::iterator) [with FragT = UnpairedRead; typename std::vector<FragT*>::iterator = __gnu_cxx::__normal_iterator<UnpairedRead**, std::vector<UnpairedRead*, std::allocator<UnpairedRead*> > >]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:466:25: required from 'void processMiniBatch(AlignmentLibrary<FragT>&, ForgettingMassCalculator&, uint64_t, MiniBatchQueue<AlignmentGroup<FragT*> >&, MiniBatchQueue<AlignmentGroup<FragT*> >*, std::condition_variable&, std::mutex&, volatile bool&, std::atomic<long unsigned int>&, const SalmonOpts&, bool&, bool, std::atomic<long unsigned int>&) [with FragT = UnpairedRead; uint64_t = long unsigned int; MiniBatchQueue<AlignmentGroup<FragT*> > = tbb::strict_ppl::concurrent_queue<MiniBatchInfo<AlignmentGroup<UnpairedRead*> >*, tbb::cache_aligned_allocator<MiniBatchInfo<AlignmentGroup<UnpairedRead*> >*> >]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:641:13: required from 'bool quantifyLibrary(AlignmentLibrary<FragT>&, std::size_t, const SalmonOpts&) [with FragT = UnpairedRead; std::size_t = long unsigned int]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1110:101: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:81:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| auto childClust = (parentClust == firstCluster) ? otherCluster : firstCluster; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:82:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (parentClust == firstCluster or parentClust == otherCluster) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:82:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (parentClust == firstCluster or parentClust == otherCluster) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp: In instantiation of 'void ClusterForest::mergeClusters(typename std::vector<FragT*>::iterator, typename std::vector<FragT*>::iterator) [with FragT = ReadPair; typename std::vector<FragT*>::iterator = __gnu_cxx::__normal_iterator<ReadPair**, std::vector<ReadPair*, std::allocator<ReadPair*> > >]': | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:466:25: required from 'void processMiniBatch(AlignmentLibrary<FragT>&, ForgettingMassCalculator&, uint64_t, MiniBatchQueue<AlignmentGroup<FragT*> >&, MiniBatchQueue<AlignmentGroup<FragT*> >*, std::condition_variable&, std::mutex&, volatile bool&, std::atomic<long unsigned int>&, const SalmonOpts&, bool&, bool, std::atomic<long unsigned int>&) [with FragT = ReadPair; uint64_t = long unsigned int; MiniBatchQueue<AlignmentGroup<FragT*> > = tbb::strict_ppl::concurrent_queue<MiniBatchInfo<AlignmentGroup<ReadPair*> >*, tbb::cache_aligned_allocator<MiniBatchInfo<AlignmentGroup<ReadPair*> >*> >]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:641:13: required from 'bool quantifyLibrary(AlignmentLibrary<FragT>&, std::size_t, const SalmonOpts&) [with FragT = ReadPair; std::size_t = long unsigned int]' | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:1156:97: required from here | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:81:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| auto childClust = (parentClust == firstCluster) ? otherCluster : firstCluster; | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:82:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (parentClust == firstCluster or parentClust == otherCluster) { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/include/ClusterForest.hpp:82:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (parentClust == firstCluster or parentClust == otherCluster) { | |
| ^ | |
| In file included from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/bam.h:58:0, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/scram.h:52, | |
| from /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src/SalmonQuantifyAlignments.cpp:3: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h: At global scope: | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:42:21: warning: 'illumina_bin' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin[256] = { | |
| ^ | |
| /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/include/io_lib/binning.h:75:21: warning: 'illumina_bin_33' defined but not used [-Wunused-variable] | |
| static unsigned int illumina_bin_33[256] = { | |
| ^ | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| cc1plus: warning: unrecognized command line option '-Wno-deprecated-register' | |
| [100%] Linking CXX executable salmon | |
| cd /tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/src && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.4.3/bin/cmake -E cmake_link_script CMakeFiles/salmon.dir/link.txt --verbose=1 | |
| /home/linuxbrew/.linuxbrew/bin/g++-5 -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -L/home/linuxbrew/.linuxbrew/lib -Wl,--dynamic-linker=/home/linuxbrew/.linuxbrew/lib/ld.so -Wl,-rpath,/home/linuxbrew/.linuxbrew/lib CMakeFiles/salmon.dir/QSufSort.c.o CMakeFiles/salmon.dir/is.c.o CMakeFiles/salmon.dir/bwt_gen.c.o CMakeFiles/salmon.dir/bwtindex.c.o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o CMakeFiles/salmon.dir/Salmon.cpp.o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o CMakeFiles/salmon.dir/SequenceBiasModel.cpp.o CMakeFiles/salmon.dir/StadenUtils.cpp.o CMakeFiles/salmon.dir/TranscriptGroup.cpp.o CMakeFiles/salmon.dir/FASTAParser.cpp.o CMakeFiles/salmon.dir/ErrorModel.cpp.o CMakeFiles/salmon.dir/AlignmentModel.cpp.o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -o salmon -L/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/lib -L/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2/external/install/lib -rdynamic libsalmon_core.a -lgff -lpthread -Wl,-Bstatic -lboost_iostreams-mt -lboost_filesystem-mt -lboost_system-mt -lboost_thread-mt -lboost_timer-mt -lboost_chrono-mt -lboost_program_options-mt -lboost_serialization-mt -Wl,-Bdynamic ../external/install/lib/libstaden-read.a -Wl,-Bstatic -lz -Wl,-Bdynamic ../external/install/lib/libjellyfish-2.0.a ../external/install/lib/libbwa.a -lm -Wl,-Bstatic -llzma -lbz2 -Wl,-Bdynamic -ltbb -ltbbmalloc -lgomp -lrt ../external/install/lib/libjemalloc.a -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" | |
| ../external/install/lib/libstaden-read.a(libstaden_read_la-open_trace_file.o): In function `find_file_url': | |
| open_trace_file.c:(.text+0xd30): warning: the use of `tempnam' is dangerous, better use `mkstemp' | |
| CMakeFiles/salmon.dir/Salmon.cpp.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const': | |
| Salmon.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)' | |
| CMakeFiles/salmon.dir/Salmon.cpp.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const': | |
| Salmon.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x27): undefined reference to `boost::program_options::arg[abi:cxx11]' | |
| CMakeFiles/salmon.dir/Salmon.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)': | |
| Salmon.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x2bc): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' | |
| Salmon.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x330): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)' | |
| CMakeFiles/salmon.dir/Salmon.cpp.o: In function `main': | |
| Salmon.cpp:(.text.startup+0x5d): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| Salmon.cpp:(.text.startup+0x18a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| Salmon.cpp:(.text.startup+0x22a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| Salmon.cpp:(.text.startup+0x950): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| CMakeFiles/salmon.dir/Salmon.cpp.o:(.data.rel.ro._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o: In function `salmonIndex(int, char**)': | |
| BuildSalmonIndex.cpp:(.text+0x3cf): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| BuildSalmonIndex.cpp:(.text+0x679): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| BuildSalmonIndex.cpp:(.text+0x72f): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| BuildSalmonIndex.cpp:(.text+0x77e): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| BuildSalmonIndex.cpp:(.text+0x7ee): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)': | |
| BuildSalmonIndex.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x26): undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)' | |
| BuildSalmonIndex.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x3c): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o: In function `boost::program_options::typed_value<unsigned int, char>::name() const': | |
| BuildSalmonIndex.cpp:(.text._ZNK5boost15program_options11typed_valueIjcE4nameEv[_ZNK5boost15program_options11typed_valueIjcE4nameEv]+0x25): undefined reference to `boost::program_options::arg[abi:cxx11]' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned int*, long)': | |
| BuildSalmonIndex.cpp:(.text._ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x738): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o:(.data.rel.ro._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o:(.data.rel.ro._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o:(.data.rel.ro._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o:(.data.rel.ro._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o:(.data.rel.ro._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o:(.data.rel.ro._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): more undefined references to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' follow | |
| CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o:(.data.rel.ro._ZTVN5boost15program_options11typed_valueIjcEE[_ZTVN5boost15program_options11typed_valueIjcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `salmonQuantify(int, char**)': | |
| SalmonQuantify.cpp:(.text+0x10bb0): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantify.cpp:(.text+0x112d0): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantify.cpp:(.text+0x118b2): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantify.cpp:(.text+0x11984): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantify.cpp:(.text+0x119fb): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantify.cpp:(.text+0x11e84): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| SalmonQuantify.cpp:(.text+0x11ef1): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| SalmonQuantify.cpp:(.text+0x11fe8): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const': | |
| SalmonQuantify.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `boost::program_options::typed_value<bool, char>::name() const': | |
| SalmonQuantify.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x25): undefined reference to `boost::program_options::arg[abi:cxx11]' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char>::name() const': | |
| SalmonQuantify.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x25): undefined reference to `boost::program_options::arg[abi:cxx11]' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `boost::program_options::typed_value<int, char>::name() const': | |
| SalmonQuantify.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[_ZNK5boost15program_options11typed_valueIicE4nameEv]+0x25): undefined reference to `boost::program_options::arg[abi:cxx11]' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `boost::program_options::typed_value<double, char>::name() const': | |
| SalmonQuantify.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameEv[_ZNK5boost15program_options11typed_valueIdcE4nameEv]+0x25): undefined reference to `boost::program_options::arg[abi:cxx11]' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `boost::program_options::typed_value<unsigned long, char>::name() const': | |
| SalmonQuantify.cpp:(.text._ZNK5boost15program_options11typed_valueImcE4nameEv[_ZNK5boost15program_options11typed_valueImcE4nameEv]+0x25): undefined reference to `boost::program_options::arg[abi:cxx11]' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `void boost::program_options::validate<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, int)': | |
| SalmonQuantify.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0xa5): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)' | |
| SalmonQuantify.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x308): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `void boost::program_options::validate<double, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)': | |
| SalmonQuantify.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x345): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long)': | |
| SalmonQuantify.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x1a5): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o: In function `void boost::program_options::validate<unsigned long, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned long*, long)': | |
| SalmonQuantify.cpp:(.text._ZN5boost15program_options8validateImcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateImcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x170): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o:(.data.rel.ro._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o:(.data.rel.ro._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o:(.data.rel.ro._ZTVN5boost15program_options11typed_valueImcEE[_ZTVN5boost15program_options11typed_valueImcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o:(.data.rel.ro._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| CMakeFiles/salmon.dir/SalmonQuantify.cpp.o:(.data.rel.ro._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o: In function `salmonAlignmentQuantify(int, char**)': | |
| SalmonQuantifyAlignments.cpp:(.text+0x23da): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantifyAlignments.cpp:(.text+0x27f4): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantifyAlignments.cpp:(.text+0x2d11): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantifyAlignments.cpp:(.text+0x2de7): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantifyAlignments.cpp:(.text+0x2e5f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| SalmonQuantifyAlignments.cpp:(.text+0x3336): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| SalmonQuantifyAlignments.cpp:(.text+0x33a7): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| SalmonQuantifyAlignments.cpp:(.text+0x3834): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| SalmonQuantifyAlignments.cpp:(.text+0x3911): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| SalmonQuantifyAlignments.cpp:(.text+0x4135): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| collect2: error: ld returned 1 exit status | |
| make[2]: *** [src/salmon] Error 1 | |
| make[2]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make[1]: *** [src/CMakeFiles/salmon.dir/all] Error 2 | |
| make[1]: Leaving directory `/tmp/salmon20160308-12341-1jdjlen/salmon-0.4.2' | |
| make: *** [all] Error 2 | |
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| PATH: /home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/linuxbrew/.linuxbrew/Library/ENV/scm |
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