{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/blasr_libcpp/issues/138","repository_url":"https://api.github.com/repos/PacificBiosciences/blasr_libcpp","labels_url":"https://api.github.com/repos/PacificBiosciences/blasr_libcpp/issues/138/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/blasr_libcpp/issues/138/comments","events_url":"https://api.github.com/repos/PacificBiosciences/blasr_libcpp/issues/138/events","html_url":"https://github.com/PacificBiosciences/blasr_libcpp/issues/138","id":142122608,"number":138,"title":"cannot compile","user":{"login":"yunfeiguo","id":7737294,"avatar_url":"https://avatars.githubusercontent.com/u/7737294?v=3","gravatar_id":"","url":"https://api.github.com/users/yunfeiguo","html_url":"https://github.com/yunfeiguo","followers_url":"https://api.github.com/users/yunfeiguo/followers","following_url":"https://api.github.com/users/yunfeiguo/following{/other_user}","gists_url":"https://api.github.com/users/yunfeiguo/gists{/gist_id}","starred_url":"https://api.github.com/users/yunfeiguo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yunfeiguo/subscriptions","organizations_url":"https://api.github.com/users/yunfeiguo/orgs","repos_url":"https://api.github.com/users/yunfeiguo/repos","events_url":"https://api.github.com/users/yunfeiguo/events{/privacy}","received_events_url":"https://api.github.com/users/yunfeiguo/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/PacificBiosciences/blasr_libcpp/labels/build","name":"build","color":"fad8c7"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2016-03-20T02:38:27Z","updated_at":"2016-03-22T00:30:15Z","closed_at":null,"body":"Hi there,\r\n\r\nI tried to complie blasr_libcpp before installing blasr, however, it always failed. Any clue? Thanks.\r\n```\r\n$ NOPBBAM=1 ./configure.py\r\nuname -s\r\nuname='Linux'\r\nwriting to '/home/yunfeiguo/Downloads/blasr_libcpp/pbdata/libconfig.h'\r\n\"\"\"\r\n\r\n\"\"\"\r\nwriting to 'defines.mk'\r\n\"\"\"\r\n\r\nSH_LIB_EXT           := .so\r\n\r\nHDF5_INC:=/home/yunfeiguo/Downloads/hdf5-1.8.15-linux-centos6-x86_64-shared/include\r\nHDF5_LIB:=/home/yunfeiguo/Downloads/hdf5-1.8.15-linux-centos6-x86_64-shared/lib\r\nLIBPBDATA_INC     ?=../pbdata\r\nLIBPBIHDF_INC     ?=../hdf\r\nLIBBLASR_INC      ?=../alignment\r\nLIBPBDATA_LIB     ?=../pbdata\r\nLIBPBIHDF_LIB     ?=../hdf\r\nLIBBLASR_LIB      ?=../alignment\r\n\r\n# Use PREFIX dir, if available.\r\nINCLUDES      += ${PREFIX_INC}\r\nLIBS          += ${PREFIX_LIB}\r\n\"\"\"\r\n\r\n$ make -j all\r\n...\r\n/home/yunfeiguo/Downloads/gcc_install/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/include/xopintrin.h: In function '__m256 _mm256_frcz_ps(__m256)':\r\n/home/yunfeiguo/Downloads/gcc_install/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/include/xopintrin.h:766:57: error: cannot convert '__m256 {aka float}' to '__vector(8) float' for argument '1' to '__vector(8) float __builtin_ia32_vfrczps256(__vector(8) float)'\r\n   return (__m256) __builtin_ia32_vfrczps256 ((__v8sf)__A);\r\n                                                         ^\r\n/home/yunfeiguo/Downloads/gcc_install/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/include/xopintrin.h: In function '__m256d _mm256_frcz_pd(__m256d)':\r\n/home/yunfeiguo/Downloads/gcc_install/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/include/xopintrin.h:772:58: error: cannot convert '__m256d {aka double}' to '__vector(4) double' for argument '1' to '__vector(4) double __builtin_ia32_vfrczpd256(__vector(4) double)'\r\n   return (__m256d) __builtin_ia32_vfrczpd256 ((__v4df)__A);\r\n                                                        ^\r\nmake[2]: *** [HDFUtils.shared.o] Error 1\r\nmake[2]: Leaving directory `/home/yunfeiguo/Downloads/blasr_libcpp/hdf'\r\nmake[1]: *** [libpbihdf] Error 2\r\nmake[1]: Leaving directory `/home/yunfeiguo/Downloads/blasr_libcpp'\r\nmake: *** [all] Error 2\r\n```"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/blasr_libcpp/issues/comments/199557108","html_url":"https://github.com/PacificBiosciences/blasr_libcpp/issues/138#issuecomment-199557108","issue_url":"https://api.github.com/repos/PacificBiosciences/blasr_libcpp/issues/138","id":199557108,"user":{"login":"yunfeiguo","id":7737294,"avatar_url":"https://avatars.githubusercontent.com/u/7737294?v=3","gravatar_id":"","url":"https://api.github.com/users/yunfeiguo","html_url":"https://github.com/yunfeiguo","followers_url":"https://api.github.com/users/yunfeiguo/followers","following_url":"https://api.github.com/users/yunfeiguo/following{/other_user}","gists_url":"https://api.github.com/users/yunfeiguo/gists{/gist_id}","starred_url":"https://api.github.com/users/yunfeiguo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yunfeiguo/subscriptions","organizations_url":"https://api.github.com/users/yunfeiguo/orgs","repos_url":"https://api.github.com/users/yunfeiguo/repos","events_url":"https://api.github.com/users/yunfeiguo/events{/privacy}","received_events_url":"https://api.github.com/users/yunfeiguo/received_events","type":"User","site_admin":false},"created_at":"2016-03-22T00:30:15Z","updated_at":"2016-03-22T00:30:15Z","body":"I installed hdf5-1.8.16 with c++ support and successfully compiled blasr! Thank both of you for your timely help!\r\n\r\nBTW, I tried pitchfork, however, it doesn't finish successfully.\r\n\r\n```\r\n$make world\r\n...\r\n<command-line>:0:0: warning: \"CHAR_CNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\ngcc -c -fPIC -I/home/yunfeiguo/Downloads/blasr/test/pitchfork/deployment/include -O2 -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=24 -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\\\"_\\\" -DCHAR_CNAME=\\\"\\\" -DNO_AFFINITY -I. -O2 -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=24 -DASMNAME=sspr2 -DASMFNAME=sspr2_ -DNAME=sspr2_ -DCNAME=sspr2 -DCHAR_NAME=\\\"sspr2_\\\" -DCHAR_CNAME=\\\"sspr2\\\" -DNO_AFFINITY -I.. -I. -UDOUBLE  -UCOMPLEX spr2.c -o sspr2.o\r\nccache: error: Failed to open /home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/.ccache/tmp/tmp.cpp_stderr.biocluster.med.usc.edu.1991.gw4CNu: No such file or directory\r\nmake[3]: *** [strmv.o] Error 1\r\nmake[3]: *** Waiting for unfinished jobs....\r\nccache: error: Failed to open /home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/.ccache/tmp/tmp.cpp_stderr.biocluster.med.usc.edu.1995.5gBd7u: No such file or directory\r\nmake[3]: *** [sgbmv.o] Error 1\r\nccache: error: Failed to open /home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/.ccache/tmp/tmp.cpp_stderr.biocluster.med.usc.edu.1993.gnuHtu: No such file or directory\r\nccache: error: Failed to open /home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/.ccache/tmp/tmp.cpp_stderr.biocluster.med.usc.edu.1997.a8152u: No such file or directory\r\nmake[3]: *** [ssyr.o] Error 1\r\nmake[3]: *** [sspmv.o] Error 1\r\nccache: error: Failed to open /home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/.ccache/tmp/tmp.cpp_stderr.biocluster.med.usc.edu.1992.x0uNIu: No such file or directory\r\nccache: error: Failed to open /home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/.ccache/tmp/tmp.cpp_stderr.biocluster.med.usc.edu.1996.fHvbov: No such file or directory\r\nccache: error: Failed to open /home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/.ccache/tmp/tmp.cpp_stderr.biocluster.med.usc.edu.1994.t4Vr6u: No such file or directory\r\nmake[3]: *** [ssymv.o] Error 1\r\nmake[3]: *** [ssbmv.o] Error 1\r\nmake[3]: *** [ssyr2.o] Error 1\r\nccache: error: Failed to open /home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/.ccache/tmp/tmp.cpp_stderr.biocluster.med.usc.edu.2000.kyJjcx: No such file or directory\r\nmake[3]: *** [sspr.o] Error 1\r\n<command-line>:0:0: warning: \"ASMNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"ASMFNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"NAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"CNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"CHAR_NAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"CHAR_CNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"ASMNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"ASMFNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"NAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"CNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"CHAR_NAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"CHAR_CNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"ASMNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"ASMFNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"NAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"CNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"CHAR_NAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\n<command-line>:0:0: warning: \"CHAR_CNAME\" redefined\r\n<command-line>:0:0: note: this is the location of the previous definition\r\nmake[3]: Leaving directory `/home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/OpenBLAS-0.2.15/interface'\r\nmake[2]: *** [libs] Error 1\r\nmake[2]: Leaving directory `/home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/OpenBLAS-0.2.15'\r\nmake[1]: *** [/home/yunfeiguo/Downloads/blasr/test/pitchfork/workspace/OpenBLAS-0.2.15/libopenblas.so] Error 1\r\nmake[1]: Leaving directory `/home/yunfeiguo/Downloads/blasr/test/pitchfork/ports/thirdparty/openblas'\r\nmake: *** [openblas] Error 2\r\n\r\n```\r\n\r\n"}}