Created
May 18, 2014 08:57
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(partial) EasyBuild log for failed build of /user/scratch/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.6/site-packages/easybuild_easyconfigs-1.13.0.0dev-py2.6.egg/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb (PR #594)
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| == 2014-05-18 10:54:05,837 main.MakeCp INFO 'This is EasyBuild 1.13.0dev (framework: 1.13.0dev, easyblocks: 1.13.0dev) on host node2153.delcatty.os.' | |
| == 2014-05-18 10:54:05,837 main.MakeCp INFO 'Init completed for application name PLINK version 1.07' | |
| == 2014-05-18 10:54:05,838 main.easyblock.<module> INFO 'Obtained application instance of for PLINK (easyblock: MakeCp)' | |
| == 2014-05-18 10:54:05,839 main.MakeCp INFO 'building and installing PLINK/1.07-ictce-5.3.0...' | |
| == 2014-05-18 10:54:05,839 main.MakeCp INFO 'fetching files...' | |
| == 2014-05-18 10:54:05,839 main.MakeCp INFO 'Starting fetch step' | |
| == 2014-05-18 10:54:05,841 main.MakeCp INFO 'Running method fetch_step part of step fetch' | |
| == 2014-05-18 10:54:05,841 main.MakeCp WARNING "Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version" | |
| == 2014-05-18 10:54:05,856 main.MakeCp INFO 'Found file plink-1.07-src.zip at /user/data/gent/vsc400/vsc40023/EasyBuild/sources/p/PLINK/plink-1.07-src.zip' | |
| == 2014-05-18 10:54:05,857 main.MakeCp INFO "Added sources: [{'path': '/user/data/gent/vsc400/vsc40023/EasyBuild/sources/p/PLINK/plink-1.07-src.zip', 'cmd': None, 'finalpath': None, 'name': 'plink-1.07-src.zip', 'checksum': None}]" | |
| == 2014-05-18 10:54:05,857 main.MakeCp INFO 'no patches provided' | |
| == 2014-05-18 10:54:05,909 main.MakeCp INFO 'md5 checksum for /user/data/gent/vsc400/vsc40023/EasyBuild/sources/p/PLINK/plink-1.07-src.zip: 4566376791df4e69459b849bd7078fa3' | |
| == 2014-05-18 10:54:05,915 main.MakeCp INFO 'Setting parallelism: 16' | |
| == 2014-05-18 10:54:05,915 main.MakeCp INFO "Checking dirs that need to be created: ['/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/PLINK', '/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/modules/all/PLINK', '/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/modules/bio/PLINK']" | |
| == 2014-05-18 10:54:05,918 main.MakeCp INFO 'creating build dir, resetting environment...' | |
| == 2014-05-18 10:54:05,919 main.MakeCp INFO 'Starting ready step' | |
| == 2014-05-18 10:54:05,920 main.MakeCp INFO 'Running method check_readiness_step part of step ready' | |
| == 2014-05-18 10:54:05,929 main.MakeCp WARNING "Loaded modules detected: ['cluster/delcatty']" | |
| == 2014-05-18 10:54:05,929 main.MakeCp INFO 'Running method gen_builddir part of step ready' | |
| == 2014-05-18 10:54:05,930 main.MakeCp INFO 'Build dir set to /tmp/vsc40023/easybuild_build/PLINK/1.07/ictce-5.3.0' | |
| == 2014-05-18 10:54:05,930 main.MakeCp INFO 'Running method gen_installdir part of step ready' | |
| == 2014-05-18 10:54:05,930 main.MakeCp INFO 'Running method make_builddir part of step ready' | |
| == 2014-05-18 10:54:05,930 main.filetools INFO 'Creating directory /tmp/vsc40023/easybuild_build/PLINK/1.07/ictce-5.3.0 (parents: True, set_gid: False, sticky: False)' | |
| == 2014-05-18 10:54:05,931 main.MakeCp INFO 'Running method env_reset_changes part of step ready' | |
| == 2014-05-18 10:54:05,931 main.MakeCp INFO 'Running method handle_iterate_opts part of step ready' | |
| == 2014-05-18 10:54:05,931 main.MakeCp INFO 'unpacking...' | |
| == 2014-05-18 10:54:05,931 main.MakeCp INFO 'Starting source step' | |
| == 2014-05-18 10:54:05,933 main.MakeCp INFO 'Running method checksum_step part of step source' | |
| == 2014-05-18 10:54:05,933 main.MakeCp INFO 'Checksum verification for /user/data/gent/vsc400/vsc40023/EasyBuild/sources/p/PLINK/plink-1.07-src.zip using None passed.' | |
| == 2014-05-18 10:54:05,933 main.MakeCp INFO 'Running method extract_step part of step source' | |
| == 2014-05-18 10:54:05,934 main.MakeCp INFO 'Unpacking source plink-1.07-src.zip' | |
| == 2014-05-18 10:54:05,978 main.MakeCp INFO 'patching...' | |
| == 2014-05-18 10:54:05,978 main.MakeCp INFO 'Starting patch step' | |
| == 2014-05-18 10:54:05,980 main.MakeCp INFO 'Running method patch_step part of step patch' | |
| == 2014-05-18 10:54:05,980 main.MakeCp INFO 'preparing...' | |
| == 2014-05-18 10:54:05,980 main.MakeCp INFO 'Starting prepare step' | |
| == 2014-05-18 10:54:05,982 main.MakeCp INFO 'Running method prepare_step part of step prepare' | |
| == 2014-05-18 10:54:31,078 main.Ictce INFO 'List of toolchain dependency modules and toolchain definition match!' | |
| == 2014-05-18 10:54:31,115 main.ToolchainOptions WARNING 'option: option with name _opt_CC returns None' | |
| == 2014-05-18 10:54:31,115 main.ToolchainOptions WARNING 'option: option with name _opt_CXX returns None' | |
| == 2014-05-18 10:54:31,115 main.ToolchainOptions WARNING 'option: option with name _opt_F77 returns None' | |
| == 2014-05-18 10:54:31,115 main.ToolchainOptions WARNING 'option: option with name _opt_F90 returns None' | |
| == 2014-05-18 10:54:31,259 main.IncludePaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/include was not found' | |
| == 2014-05-18 10:54:31,260 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib64 was not found' | |
| == 2014-05-18 10:54:31,260 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib was not found' | |
| == 2014-05-18 10:54:31,327 main.IncludePaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/include was not found' | |
| == 2014-05-18 10:54:31,329 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib64 was not found' | |
| == 2014-05-18 10:54:31,329 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib was not found' | |
| == 2014-05-18 10:54:31,352 main.IncludePaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/include was not found' | |
| == 2014-05-18 10:54:31,354 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib64 was not found' | |
| == 2014-05-18 10:54:31,354 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib was not found' | |
| == 2014-05-18 10:54:31,418 main.IncludePaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/include was not found' | |
| == 2014-05-18 10:54:31,420 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib64 was not found' | |
| == 2014-05-18 10:54:31,420 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib was not found' | |
| == 2014-05-18 10:54:31,423 main.tools.utilities.<module> WARNING 'Deprecated functionality, will no longer work in v2.0: own definition of any' | |
| == 2014-05-18 10:54:31,425 main.tools.utilities.<module> WARNING 'Deprecated functionality, will no longer work in v2.0: own definition of any' | |
| == 2014-05-18 10:54:31,426 main.tools.utilities.<module> WARNING 'Deprecated functionality, will no longer work in v2.0: own definition of any' | |
| == 2014-05-18 10:54:31,428 main.tools.utilities.<module> WARNING 'Deprecated functionality, will no longer work in v2.0: own definition of any' | |
| == 2014-05-18 10:54:31,428 main.tools.utilities.<module> WARNING 'Deprecated functionality, will no longer work in v2.0: own definition of all' | |
| == 2014-05-18 10:54:31,449 main.IncludePaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/include was not found' | |
| == 2014-05-18 10:54:31,450 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib64 was not found' | |
| == 2014-05-18 10:54:31,451 main.LinkLibraryPaths WARNING 'flags_for_subdirs: directory /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/lib was not found' | |
| == 2014-05-18 10:54:31,466 main.environment INFO 'Environment variable CPPFLAGS set to -I/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,467 main.environment INFO 'Environment variable EBVARCPPFLAGS set to -I/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,467 main.environment INFO 'Environment variable I_MPI_CC set to icc' | |
| == 2014-05-18 10:54:31,467 main.environment INFO 'Environment variable EBVARI_MPI_CC set to icc' | |
| == 2014-05-18 10:54:31,467 main.environment INFO 'Environment variable MPI_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/impi/4.1.0.030/include64' | |
| == 2014-05-18 10:54:31,467 main.environment INFO 'Environment variable EBVARMPI_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/impi/4.1.0.030/include64' | |
| == 2014-05-18 10:54:31,467 main.environment INFO 'Environment variable BLAS_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,468 main.environment INFO 'Environment variable EBVARBLAS_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,468 main.environment INFO 'Environment variable LIBSCALAPACK set to -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,468 main.environment INFO 'Environment variable EBVARLIBSCALAPACK set to -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,468 main.environment INFO 'Environment variable MPI_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/impi/4.1.0.030/lib64' | |
| == 2014-05-18 10:54:31,468 main.environment INFO 'Environment variable EBVARMPI_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/impi/4.1.0.030/lib64' | |
| == 2014-05-18 10:54:31,468 main.environment INFO 'Environment variable LAPACK_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,469 main.environment INFO 'Environment variable EBVARLAPACK_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,469 main.environment INFO 'Environment variable MPI_LIB_STATIC set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/impi/4.1.0.030/lib64/libmpi.a' | |
| == 2014-05-18 10:54:31,469 main.environment INFO 'Environment variable EBVARMPI_LIB_STATIC set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/impi/4.1.0.030/lib64/libmpi.a' | |
| == 2014-05-18 10:54:31,469 main.environment INFO 'Environment variable CXXFLAGS set to -O2 -xHOST -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,469 main.environment INFO 'Environment variable EBVARCXXFLAGS set to -O2 -xHOST -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,470 main.environment INFO 'Environment variable I_MPI_F90 set to ifort' | |
| == 2014-05-18 10:54:31,470 main.environment INFO 'Environment variable EBVARI_MPI_F90 set to ifort' | |
| == 2014-05-18 10:54:31,470 main.environment INFO 'Environment variable MPICC set to mpicc' | |
| == 2014-05-18 10:54:31,470 main.environment INFO 'Environment variable EBVARMPICC set to mpicc' | |
| == 2014-05-18 10:54:31,470 main.environment INFO 'Environment variable FFT_STATIC_LIBS set to libfftw3xc_intel.a,libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,470 main.environment INFO 'Environment variable EBVARFFT_STATIC_LIBS set to libfftw3xc_intel.a,libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,471 main.environment INFO 'Environment variable LIBS set to -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,471 main.environment INFO 'Environment variable EBVARLIBS set to -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,471 main.environment INFO 'Environment variable LIBLAPACK set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,471 main.environment INFO 'Environment variable EBVARLIBLAPACK set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,471 main.environment INFO 'Environment variable SCALAPACK_LIB_DIR set to ' | |
| == 2014-05-18 10:54:31,471 main.environment INFO 'Environment variable EBVARSCALAPACK_LIB_DIR set to ' | |
| == 2014-05-18 10:54:31,472 main.environment INFO 'Environment variable FFTW_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,472 main.environment INFO 'Environment variable EBVARFFTW_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,472 main.environment INFO 'Environment variable LIBSCALAPACK_MT_ONLY set to -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,472 main.environment INFO 'Environment variable EBVARLIBSCALAPACK_MT_ONLY set to -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,472 main.environment INFO 'Environment variable BLAS_LAPACK_MT_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_intel_thread.a,libmkl_core.a,libiomp5.a,libpthread.a' | |
| == 2014-05-18 10:54:31,472 main.environment INFO 'Environment variable EBVARBLAS_LAPACK_MT_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_intel_thread.a,libmkl_core.a,libiomp5.a,libpthread.a' | |
| == 2014-05-18 10:54:31,473 main.environment INFO 'Environment variable LIBLAPACK_MT set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,473 main.environment INFO 'Environment variable EBVARLIBLAPACK_MT set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,473 main.environment INFO 'Environment variable LIBSCALAPACK_MT set to -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,473 main.environment INFO 'Environment variable EBVARLIBSCALAPACK_MT set to -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,473 main.environment INFO 'Environment variable I_MPI_F77 set to ifort' | |
| == 2014-05-18 10:54:31,473 main.environment INFO 'Environment variable EBVARI_MPI_F77 set to ifort' | |
| == 2014-05-18 10:54:31,474 main.environment INFO 'Environment variable FFTW_STATIC_LIBS set to libfftw3xc_intel.a,libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,474 main.environment INFO 'Environment variable EBVARFFTW_STATIC_LIBS set to libfftw3xc_intel.a,libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,474 main.environment INFO 'Environment variable BLAS_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,474 main.environment INFO 'Environment variable EBVARBLAS_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,474 main.environment INFO 'Environment variable SCALAPACK_MT_STATIC_LIBS set to libmkl_scalapack_lp64.a,libmkl_blacs_intelmpi_lp64.a,libmkl_intel_lp64.a,libmkl_intel_thread.a,libmkl_core.a,libiomp5.a,libpthread.a' | |
| == 2014-05-18 10:54:31,474 main.environment INFO 'Environment variable EBVARSCALAPACK_MT_STATIC_LIBS set to libmkl_scalapack_lp64.a,libmkl_blacs_intelmpi_lp64.a,libmkl_intel_lp64.a,libmkl_intel_thread.a,libmkl_core.a,libiomp5.a,libpthread.a' | |
| == 2014-05-18 10:54:31,475 main.environment INFO 'Environment variable SCALAPACK_INC_DIR set to ' | |
| == 2014-05-18 10:54:31,475 main.environment INFO 'Environment variable EBVARSCALAPACK_INC_DIR set to ' | |
| == 2014-05-18 10:54:31,475 main.environment INFO 'Environment variable F90 set to ifort' | |
| == 2014-05-18 10:54:31,475 main.environment INFO 'Environment variable EBVARF90 set to ifort' | |
| == 2014-05-18 10:54:31,475 main.environment INFO 'Environment variable LIBSCALAPACK_ONLY set to -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,475 main.environment INFO 'Environment variable EBVARLIBSCALAPACK_ONLY set to -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_lp64 -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,476 main.environment INFO 'Environment variable F90FLAGS set to -O2 -xHOST -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,476 main.environment INFO 'Environment variable EBVARF90FLAGS set to -O2 -xHOST -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,476 main.environment INFO 'Environment variable MPICXX set to mpicxx' | |
| == 2014-05-18 10:54:31,476 main.environment INFO 'Environment variable EBVARMPICXX set to mpicxx' | |
| == 2014-05-18 10:54:31,476 main.environment INFO 'Environment variable LAPACK_MT_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_intel_thread.a,libmkl_core.a,libiomp5.a,libpthread.a' | |
| == 2014-05-18 10:54:31,476 main.environment INFO 'Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_intel_thread.a,libmkl_core.a,libiomp5.a,libpthread.a' | |
| == 2014-05-18 10:54:31,477 main.environment INFO 'Environment variable BLACS_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,477 main.environment INFO 'Environment variable EBVARBLACS_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,477 main.environment INFO 'Environment variable BLAS_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,477 main.environment INFO 'Environment variable EBVARBLAS_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,477 main.environment INFO 'Environment variable FFT_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,478 main.environment INFO 'Environment variable EBVARFFT_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,478 main.environment INFO 'Environment variable LIBFFT set to -Wl,-Bstatic -Wl,--start-group -lfftw3xc_intel -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,478 main.environment INFO 'Environment variable EBVARLIBFFT set to -Wl,-Bstatic -Wl,--start-group -lfftw3xc_intel -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,478 main.environment INFO 'Environment variable BLACS_MT_STATIC_LIBS set to libmkl_blacs_intelmpi_lp64.a' | |
| == 2014-05-18 10:54:31,478 main.environment INFO 'Environment variable EBVARBLACS_MT_STATIC_LIBS set to libmkl_blacs_intelmpi_lp64.a' | |
| == 2014-05-18 10:54:31,478 main.environment INFO 'Environment variable CC set to icc' | |
| == 2014-05-18 10:54:31,479 main.environment INFO 'Environment variable EBVARCC set to icc' | |
| == 2014-05-18 10:54:31,479 main.environment INFO 'Environment variable FFLAGS set to -O2 -xHOST -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,479 main.environment INFO 'Environment variable EBVARFFLAGS set to -O2 -xHOST -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,479 main.environment INFO 'Environment variable MPICH_CXX set to icpc' | |
| == 2014-05-18 10:54:31,479 main.environment INFO 'Environment variable EBVARMPICH_CXX set to icpc' | |
| == 2014-05-18 10:54:31,479 main.environment INFO 'Environment variable MPIF90 set to mpif90' | |
| == 2014-05-18 10:54:31,480 main.environment INFO 'Environment variable EBVARMPIF90 set to mpif90' | |
| == 2014-05-18 10:54:31,480 main.environment INFO 'Environment variable LAPACK_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,480 main.environment INFO 'Environment variable EBVARLAPACK_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,480 main.environment INFO 'Environment variable MPIF77 set to mpif77' | |
| == 2014-05-18 10:54:31,480 main.environment INFO 'Environment variable EBVARMPIF77 set to mpif77' | |
| == 2014-05-18 10:54:31,480 main.environment INFO 'Environment variable MPICH_F90 set to ifort' | |
| == 2014-05-18 10:54:31,481 main.environment INFO 'Environment variable EBVARMPICH_F90 set to ifort' | |
| == 2014-05-18 10:54:31,481 main.environment INFO 'Environment variable LIBBLACS set to -Wl,-Bstatic -Wl,--start-group -lmkl_blacs_intelmpi_lp64 -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,481 main.environment INFO 'Environment variable EBVARLIBBLACS set to -Wl,-Bstatic -Wl,--start-group -lmkl_blacs_intelmpi_lp64 -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,481 main.environment INFO 'Environment variable LIBBLAS_MT set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,481 main.environment INFO 'Environment variable EBVARLIBBLAS_MT set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,481 main.environment INFO 'Environment variable LIBBLAS set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,482 main.environment INFO 'Environment variable EBVARLIBBLAS set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,482 main.environment INFO 'Environment variable BLAS_LAPACK_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,482 main.environment INFO 'Environment variable EBVARBLAS_LAPACK_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,482 main.environment INFO 'Environment variable OPTFLAGS set to -O2 -xHOST' | |
| == 2014-05-18 10:54:31,482 main.environment INFO 'Environment variable EBVAROPTFLAGS set to -O2 -xHOST' | |
| == 2014-05-18 10:54:31,482 main.environment INFO 'Environment variable BLACS_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,483 main.environment INFO 'Environment variable EBVARBLACS_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,483 main.environment INFO 'Environment variable MPICH_CC set to icc' | |
| == 2014-05-18 10:54:31,483 main.environment INFO 'Environment variable EBVARMPICH_CC set to icc' | |
| == 2014-05-18 10:54:31,483 main.environment INFO 'Environment variable F77 set to ifort' | |
| == 2014-05-18 10:54:31,483 main.environment INFO 'Environment variable EBVARF77 set to ifort' | |
| == 2014-05-18 10:54:31,483 main.environment INFO 'Environment variable BLACS_STATIC_LIBS set to libmkl_blacs_intelmpi_lp64.a' | |
| == 2014-05-18 10:54:31,484 main.environment INFO 'Environment variable EBVARBLACS_STATIC_LIBS set to libmkl_blacs_intelmpi_lp64.a' | |
| == 2014-05-18 10:54:31,484 main.environment INFO 'Environment variable FFT_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,484 main.environment INFO 'Environment variable EBVARFFT_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,484 main.environment INFO 'Environment variable LIBBLACS_MT set to -Wl,-Bstatic -Wl,--start-group -lmkl_blacs_intelmpi_lp64 -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,484 main.environment INFO 'Environment variable EBVARLIBBLACS_MT set to -Wl,-Bstatic -Wl,--start-group -lmkl_blacs_intelmpi_lp64 -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,485 main.environment INFO 'Environment variable LAPACK_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,485 main.environment INFO 'Environment variable EBVARLAPACK_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,485 main.environment INFO 'Environment variable BLAS_LAPACK_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,485 main.environment INFO 'Environment variable EBVARBLAS_LAPACK_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,485 main.environment INFO 'Environment variable LIBLAPACK_ONLY set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,485 main.environment INFO 'Environment variable EBVARLIBLAPACK_ONLY set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -Wl,-Bdynamic' | |
| == 2014-05-18 10:54:31,486 main.environment INFO 'Environment variable LIBLAPACK_MT_ONLY set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,486 main.environment INFO 'Environment variable EBVARLIBLAPACK_MT_ONLY set to -Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread' | |
| == 2014-05-18 10:54:31,486 main.environment INFO 'Environment variable MPICH_F77 set to ifort' | |
| == 2014-05-18 10:54:31,486 main.environment INFO 'Environment variable EBVARMPICH_F77 set to ifort' | |
| == 2014-05-18 10:54:31,486 main.environment INFO 'Environment variable LDFLAGS set to -L/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/icc/2013.3.163/compiler/lib/intel64 -L/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64 -L/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/compiler/lib/intel64' | |
| == 2014-05-18 10:54:31,486 main.environment INFO 'Environment variable EBVARLDFLAGS set to -L/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/icc/2013.3.163/compiler/lib/intel64 -L/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64 -L/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/compiler/lib/intel64' | |
| == 2014-05-18 10:54:31,487 main.environment INFO 'Environment variable CXX set to icpc' | |
| == 2014-05-18 10:54:31,487 main.environment INFO 'Environment variable EBVARCXX set to icpc' | |
| == 2014-05-18 10:54:31,487 main.environment INFO 'Environment variable BLAS_LAPACK_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,487 main.environment INFO 'Environment variable EBVARBLAS_LAPACK_INC_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/include' | |
| == 2014-05-18 10:54:31,487 main.environment INFO 'Environment variable I_MPI_CXX set to icpc' | |
| == 2014-05-18 10:54:31,487 main.environment INFO 'Environment variable EBVARI_MPI_CXX set to icpc' | |
| == 2014-05-18 10:54:31,488 main.environment INFO 'Environment variable MPI_LIB_SHARED set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/impi/4.1.0.030/lib64/libmpi.so' | |
| == 2014-05-18 10:54:31,488 main.environment INFO 'Environment variable EBVARMPI_LIB_SHARED set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/impi/4.1.0.030/lib64/libmpi.so' | |
| == 2014-05-18 10:54:31,488 main.environment INFO 'Environment variable SCALAPACK_STATIC_LIBS set to libmkl_scalapack_lp64.a,libmkl_blacs_intelmpi_lp64.a,libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,488 main.environment INFO 'Environment variable EBVARSCALAPACK_STATIC_LIBS set to libmkl_scalapack_lp64.a,libmkl_blacs_intelmpi_lp64.a,libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a' | |
| == 2014-05-18 10:54:31,488 main.environment INFO 'Environment variable CFLAGS set to -O2 -xHOST -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,488 main.environment INFO 'Environment variable EBVARCFLAGS set to -O2 -xHOST -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,489 main.environment INFO 'Environment variable BLAS_MT_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_intel_thread.a,libmkl_core.a,libiomp5.a,libpthread.a' | |
| == 2014-05-18 10:54:31,489 main.environment INFO 'Environment variable EBVARBLAS_MT_STATIC_LIBS set to libmkl_intel_lp64.a,libmkl_intel_thread.a,libmkl_core.a,libiomp5.a,libpthread.a' | |
| == 2014-05-18 10:54:31,489 main.environment INFO 'Environment variable PRECFLAGS set to -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,489 main.environment INFO 'Environment variable EBVARPRECFLAGS set to -ftz -fp-speculation=safe -fp-model source' | |
| == 2014-05-18 10:54:31,489 main.environment INFO 'Environment variable FFTW_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,489 main.environment INFO 'Environment variable EBVARFFTW_LIB_DIR set to /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/imkl/11.0.3.163/mkl/lib/intel64' | |
| == 2014-05-18 10:54:31,490 main.MakeCp INFO 'configuring...' | |
| == 2014-05-18 10:54:31,490 main.MakeCp INFO 'Starting configure step' | |
| == 2014-05-18 10:54:31,492 main.MakeCp INFO 'Running method configure_step part of step configure' | |
| == 2014-05-18 10:54:31,492 main.MakeCp INFO 'building...' | |
| == 2014-05-18 10:54:31,492 main.MakeCp INFO 'Starting build step' | |
| == 2014-05-18 10:54:31,493 main.MakeCp INFO 'Running method build_step part of step build' | |
| == 2014-05-18 10:54:55,489 main.run ERROR 'EasyBuild crashed with an error (at easybuild/tools/run.py:382 in parse_cmd_output): cmd " make -j 16 " exited with exitcode 2 and output:\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c plink.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c options.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c input.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c binput.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c tinput.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c genome.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c helper.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c stats.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c filters.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c locus.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c multi.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c crandom.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c cluster.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c mds.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c output.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c informative.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c assoc.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c epi.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c prephap.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c phase.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c trio.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c tdt.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c sharing.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c genepi.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c sets.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c perm.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c mh.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c genedrop.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c gxe.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c merge.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c hotel.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c multiple.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c haploCC.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c haploTDT.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c poo.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c webcheck.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c qfam.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c linear.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c bmerge.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c parse.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c mishap.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c legacy.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c homozyg.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c segment.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c model.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c logistic.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c glm.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c dcdflib.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c elf.cpp\ndcdflib.cpp: In function \xe2\x80\x98void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)\xe2\x80\x99:\ndcdflib.cpp:6025: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\ndcdflib.cpp: In function \xe2\x80\x98double dlanor(double*)\xe2\x80\x99:\ndcdflib.cpp:6401: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\ndcdflib.cpp: In function \xe2\x80\x98double dstrem(double*)\xe2\x80\x99:\ndcdflib.cpp:6782: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c dfam.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c fisher.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c linput.cpp\nfisher.cpp: In function \xe2\x80\x98void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)\xe2\x80\x99:\nfisher.cpp:261: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp:267: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp:273: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp: In function \xe2\x80\x98void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)\xe2\x80\x99:\nfisher.cpp:448: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp:450: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp:501: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp:509: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp:563: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp:751: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp: In function \xe2\x80\x98void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)\xe2\x80\x99:\nfisher.cpp:1539: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp:1555: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp:1597: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp: In function \xe2\x80\x98int iwork(int, int*, int, int)\xe2\x80\x99:\nfisher.cpp:2001: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nfisher.cpp: In function \xe2\x80\x98void isort(int*, int*)\xe2\x80\x99:\nfisher.cpp:2078: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c sockets.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c lookup.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c proxy.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c pdriver.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c haploQTL.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c haplohelper.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c haplowindow.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c genogroup.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c nonfounderphasing.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c clumpld.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c genoerr.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c em.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c impute.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c metaem.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c profile.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c nlist.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c whap.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c simul.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c gvar.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c cnv.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c step.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c greport.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c flip.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c qualscores.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c cnvqt.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c cfamily.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c setscreen.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c idhelp.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c tag.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c hapglm.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c lookup2.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c blox.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c zed.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c dosage.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c annot.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c metaanal.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c r.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c Rconnection.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c zfstream.cpp\nIn file included from Rconnection.cpp:30:\nRconnection.h: In constructor \xe2\x80\x98Rsymbol::Rsymbol(Rmessage*)\xe2\x80\x99:\nRconnection.h:203: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nRconnection.h: In constructor \xe2\x80\x98Rsymbol::Rsymbol(unsigned int*, Rmessage*)\xe2\x80\x99:\nRconnection.h:206: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nRconnection.cpp: At global scope:\nRconnection.cpp:56: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nIn file included from r.cpp:29:\nRconnection.h: In constructor \xe2\x80\x98Rsymbol::Rsymbol(Rmessage*)\xe2\x80\x99:\nRconnection.h:203: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\nRconnection.h: In constructor \xe2\x80\x98Rsymbol::Rsymbol(unsigned int*, Rmessage*)\xe2\x80\x99:\nRconnection.h:206: warning: deprecated conversion from string constant to \xe2\x80\x98char*\xe2\x80\x99\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz \n/usr/bin/ld: cannot find -lz\ncollect2: ld returned 1 exit status\nmake: *** [plink] Error 1\n' | |
| == 2014-05-18 10:54:55,489 main.easyblock.<module> WARNING 'build failed (first 300 chars): EasyBuild crashed with an error (at easybuild/tools/run.py:382 in parse_cmd_output): cmd " make -j 16 " exited with exitcode 2 and output:\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c plink.cpp\ng++ -O3 -I. -DUNIX -static -DWITH_R_PLUGINS -DWITH_ZLIB -c options.cpp\ng++ -O3 -I. -DUNIX' | |
| == 2014-05-18 10:54:55,489 main.MakeCp INFO 'Closing log for application name PLINK version 1.07' |
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