Created
August 8, 2014 12:30
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(partial) EasyBuild log for failed build of /tmp/easybuild-s1d0E3/files_pr960/Celera_Assembler-8.1-goolf-1.4.10.eb (PR #960)
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| == 2014-08-08 14:29:09,583 main.environment INFO Environment variable FFT_INC_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/FFTW/3.3.3-gompi-1.4.10/include | |
| == 2014-08-08 14:29:09,584 main.environment INFO Environment variable EBVARFFT_INC_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/FFTW/3.3.3-gompi-1.4.10/include | |
| == 2014-08-08 14:29:09,584 main.Goolf DEBUG _setenv_variables: setting environment variable LAPACK_MT_STATIC_LIBS to libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,584 main.environment INFO Environment variable LAPACK_MT_STATIC_LIBS set to libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,585 main.environment INFO Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,585 main.Goolf DEBUG _setenv_variables: setting environment variable LAPACK_LIB_DIR to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib | |
| == 2014-08-08 14:29:09,586 main.environment INFO Environment variable LAPACK_LIB_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib | |
| == 2014-08-08 14:29:09,586 main.environment INFO Environment variable EBVARLAPACK_LIB_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib | |
| == 2014-08-08 14:29:09,586 main.Goolf DEBUG _setenv_variables: setting environment variable BLAS_LAPACK_STATIC_LIBS to libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,587 main.environment INFO Environment variable BLAS_LAPACK_STATIC_LIBS set to libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,587 main.environment INFO Environment variable EBVARBLAS_LAPACK_STATIC_LIBS set to libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,588 main.Goolf DEBUG _setenv_variables: setting environment variable LIBLAPACK_ONLY to -lopenblas -lgfortran | |
| == 2014-08-08 14:29:09,588 main.environment INFO Environment variable LIBLAPACK_ONLY set to -lopenblas -lgfortran | |
| == 2014-08-08 14:29:09,589 main.environment INFO Environment variable EBVARLIBLAPACK_ONLY set to -lopenblas -lgfortran | |
| == 2014-08-08 14:29:09,589 main.Goolf DEBUG _setenv_variables: setting environment variable LIBLAPACK_MT_ONLY to -lopenblas -lgfortran | |
| == 2014-08-08 14:29:09,589 main.environment INFO Environment variable LIBLAPACK_MT_ONLY set to -lopenblas -lgfortran | |
| == 2014-08-08 14:29:09,590 main.environment INFO Environment variable EBVARLIBLAPACK_MT_ONLY set to -lopenblas -lgfortran | |
| == 2014-08-08 14:29:09,590 main.Goolf DEBUG _setenv_variables: setting environment variable LDFLAGS to -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/GCC/4.7.2/lib64 -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/GCC/4.7.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/FFTW/3.3.3-gompi-1.4.10/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/bzip2/1.0.6-goolf-1.4.10/lib | |
| == 2014-08-08 14:29:09,591 main.environment INFO Environment variable LDFLAGS set to -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/GCC/4.7.2/lib64 -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/GCC/4.7.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/FFTW/3.3.3-gompi-1.4.10/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/bzip2/1.0.6-goolf-1.4.10/lib | |
| == 2014-08-08 14:29:09,591 main.environment INFO Environment variable EBVARLDFLAGS set to -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/GCC/4.7.2/lib64 -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/GCC/4.7.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/FFTW/3.3.3-gompi-1.4.10/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/bzip2/1.0.6-goolf-1.4.10/lib | |
| == 2014-08-08 14:29:09,591 main.Goolf DEBUG _setenv_variables: setting environment variable CXX to g++ | |
| == 2014-08-08 14:29:09,592 main.environment INFO Environment variable CXX set to g++ | |
| == 2014-08-08 14:29:09,592 main.environment INFO Environment variable EBVARCXX set to g++ | |
| == 2014-08-08 14:29:09,593 main.Goolf DEBUG _setenv_variables: setting environment variable BLAS_LAPACK_INC_DIR to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/include | |
| == 2014-08-08 14:29:09,593 main.environment INFO Environment variable BLAS_LAPACK_INC_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/include | |
| == 2014-08-08 14:29:09,594 main.environment INFO Environment variable EBVARBLAS_LAPACK_INC_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/include | |
| == 2014-08-08 14:29:09,594 main.Goolf DEBUG _setenv_variables: setting environment variable OMPI_FC to gfortran | |
| == 2014-08-08 14:29:09,594 main.environment INFO Environment variable OMPI_FC set to gfortran | |
| == 2014-08-08 14:29:09,595 main.environment INFO Environment variable EBVAROMPI_FC set to gfortran | |
| == 2014-08-08 14:29:09,595 main.Goolf DEBUG _setenv_variables: setting environment variable BLAS_INC_DIR to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/include | |
| == 2014-08-08 14:29:09,596 main.environment INFO Environment variable BLAS_INC_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/include | |
| == 2014-08-08 14:29:09,596 main.environment INFO Environment variable EBVARBLAS_INC_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/include | |
| == 2014-08-08 14:29:09,596 main.Goolf DEBUG _setenv_variables: setting environment variable MPI_LIB_SHARED to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi.so | |
| == 2014-08-08 14:29:09,597 main.environment INFO Environment variable MPI_LIB_SHARED set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi.so | |
| == 2014-08-08 14:29:09,597 main.environment INFO Environment variable EBVARMPI_LIB_SHARED set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi.so | |
| == 2014-08-08 14:29:09,598 main.Goolf DEBUG _setenv_variables: setting environment variable SCALAPACK_STATIC_LIBS to libscalapack.a,libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,598 main.environment INFO Environment variable SCALAPACK_STATIC_LIBS set to libscalapack.a,libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,598 main.environment INFO Environment variable EBVARSCALAPACK_STATIC_LIBS set to libscalapack.a,libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,599 main.Goolf DEBUG _setenv_variables: setting environment variable CFLAGS to -O2 -march=native | |
| == 2014-08-08 14:29:09,599 main.environment INFO Environment variable CFLAGS set to -O2 -march=native | |
| == 2014-08-08 14:29:09,600 main.environment INFO Environment variable EBVARCFLAGS set to -O2 -march=native | |
| == 2014-08-08 14:29:09,600 main.Goolf DEBUG _setenv_variables: setting environment variable BLAS_MT_STATIC_LIBS to libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,601 main.environment INFO Environment variable BLAS_MT_STATIC_LIBS set to libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,601 main.environment INFO Environment variable EBVARBLAS_MT_STATIC_LIBS set to libopenblas.a,libgfortran.a | |
| == 2014-08-08 14:29:09,601 main.Goolf DEBUG _setenv_variables: setting environment variable FFTW_LIB_DIR to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/FFTW/3.3.3-gompi-1.4.10/lib | |
| == 2014-08-08 14:29:09,602 main.environment INFO Environment variable FFTW_LIB_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/FFTW/3.3.3-gompi-1.4.10/lib | |
| == 2014-08-08 14:29:09,602 main.environment INFO Environment variable EBVARFFTW_LIB_DIR set to /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/FFTW/3.3.3-gompi-1.4.10/lib | |
| == 2014-08-08 14:29:09,603 main.Goolf DEBUG _setenv_variables: setting environment variable OMPI_CXX to g++ | |
| == 2014-08-08 14:29:09,603 main.environment INFO Environment variable OMPI_CXX set to g++ | |
| == 2014-08-08 14:29:09,603 main.environment INFO Environment variable EBVAROMPI_CXX set to g++ | |
| == 2014-08-08 14:29:09,604 main.MakeCp DEBUG Changed to real build directory /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/ | |
| == 2014-08-08 14:29:09,604 main.MakeCp INFO configuring... | |
| == 2014-08-08 14:29:09,605 main.MakeCp INFO Starting configure step | |
| == 2014-08-08 14:29:09,607 main.easyconfig.templates DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'configure_cmd_prefix': ['', 'Prefix to be glued before ./configure', (1, 'easyblock-specific')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'prebuildopts': ['cd kmer && make install && cd .. && cd samtools && make && cd .. && cd src && ', 'Extra options pre-passed to build command.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'runtest': [None, 'Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test)', (3, 'build')], 'sources': [['wgs-%(version)s.tar.bz2'], 'List of source files', (3, 'build')], 'versionsuffix': ['', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': [None, 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'patches': [[], 'List of patches to apply', (3, 'build')], 'with_configure': [False, 'Run configure script before building', (3, 'build')], 'postinstallcmds': [[], 'Commands to run after the install step.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'start_dir': ['/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['8.1', 'Version of software', (0, 'mandatory')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'homepage': ['http://wgs-assembler.sourceforge.net/', 'The homepage of the software', (0, 'mandatory')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'tar_config_opts': [False, 'Override tar settings as determined by configure.', (1, 'easyblock-specific')], 'description': [' Celera Assembler is a de novo whole-genome shotgun (WGS) DNA \n sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary \n data produced by whole-genome shotgun sequencing. ', 'A short description of the software', (0, 'mandatory')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'source_urls': [[('http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-%(version)s/', 'download')], 'List of URLs for source files', (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'dummy': False, 'toolchain': {'version': '1.4.10', 'name': 'goolf'}, 'name': 'bzip2', 'versionsuffix': '', 'version': '1.0.6', 'mod_name': 'bzip2/1.0.6-goolf-1.4.10'}], 'List of dependencies', (5, 'dependencies')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')], 'key': [None, 'Key for installing software', (6, 'license')], 'prefix_opt': ['--prefix=', 'Prefix command line option for configure script', (1, 'easyblock-specific')], 'toolchain': [{'version': '1.4.10', 'name': 'goolf'}, 'Name and version of toolchain', (0, 'mandatory')], 'parallel': [1, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'sanity_check_paths': [{'files': ['bin/bogus', 'bin/convert-fasta-to-v2.pl', 'bin/fastqAnalyze', 'bin/markUniqueUnique', 'bin/pacBioToCA', 'bin/uidclient'], 'dirs': ['lib']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['Celera_Assembler', 'Name of software', (0, 'mandatory')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'preconfigopts': ['', 'Extra options pre-passed to configure.', (3, 'build')], 'easyblock': ['MakeCp', 'EasyBlock to use for building', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'files_to_copy': [['Linux-amd64/*'], 'List of files or dirs to copy', (0, 'mandatory')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')]} | |
| == 2014-08-08 14:29:09,610 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,611 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,611 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,612 main.easyconfig.templates DEBUG name: name, config: Celera_Assembler | |
| == 2014-08-08 14:29:09,612 main.easyconfig.templates DEBUG name: version, config: 8.1 | |
| == 2014-08-08 14:29:09,612 main.easyconfig.templates DEBUG name: versionsuffix, config: | |
| == 2014-08-08 14:29:09,613 main.easyconfig.templates DEBUG name: versionprefix, config: | |
| == 2014-08-08 14:29:09,615 main.easyconfig.templates DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'configure_cmd_prefix': ['', 'Prefix to be glued before ./configure', (1, 'easyblock-specific')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'prebuildopts': ['cd kmer && make install && cd .. && cd samtools && make && cd .. && cd src && ', 'Extra options pre-passed to build command.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'runtest': [None, 'Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test)', (3, 'build')], 'sources': [['wgs-%(version)s.tar.bz2'], 'List of source files', (3, 'build')], 'versionsuffix': ['', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': [None, 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'patches': [[], 'List of patches to apply', (3, 'build')], 'with_configure': [False, 'Run configure script before building', (3, 'build')], 'postinstallcmds': [[], 'Commands to run after the install step.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'start_dir': ['/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['8.1', 'Version of software', (0, 'mandatory')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'homepage': ['http://wgs-assembler.sourceforge.net/', 'The homepage of the software', (0, 'mandatory')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'tar_config_opts': [False, 'Override tar settings as determined by configure.', (1, 'easyblock-specific')], 'description': [' Celera Assembler is a de novo whole-genome shotgun (WGS) DNA \n sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary \n data produced by whole-genome shotgun sequencing. ', 'A short description of the software', (0, 'mandatory')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'source_urls': [[('http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-%(version)s/', 'download')], 'List of URLs for source files', (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'dummy': False, 'toolchain': {'version': '1.4.10', 'name': 'goolf'}, 'name': 'bzip2', 'versionsuffix': '', 'version': '1.0.6', 'mod_name': 'bzip2/1.0.6-goolf-1.4.10'}], 'List of dependencies', (5, 'dependencies')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')], 'key': [None, 'Key for installing software', (6, 'license')], 'prefix_opt': ['--prefix=', 'Prefix command line option for configure script', (1, 'easyblock-specific')], 'toolchain': [{'version': '1.4.10', 'name': 'goolf'}, 'Name and version of toolchain', (0, 'mandatory')], 'parallel': [1, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'sanity_check_paths': [{'files': ['bin/bogus', 'bin/convert-fasta-to-v2.pl', 'bin/fastqAnalyze', 'bin/markUniqueUnique', 'bin/pacBioToCA', 'bin/uidclient'], 'dirs': ['lib']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['Celera_Assembler', 'Name of software', (0, 'mandatory')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'preconfigopts': ['', 'Extra options pre-passed to configure.', (3, 'build')], 'easyblock': ['MakeCp', 'EasyBlock to use for building', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'files_to_copy': [['Linux-amd64/*'], 'List of files or dirs to copy', (0, 'mandatory')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')]} | |
| == 2014-08-08 14:29:09,618 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,618 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,619 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,619 main.easyconfig.templates DEBUG name: name, config: Celera_Assembler | |
| == 2014-08-08 14:29:09,620 main.easyconfig.templates DEBUG name: version, config: 8.1 | |
| == 2014-08-08 14:29:09,620 main.easyconfig.templates DEBUG name: versionsuffix, config: | |
| == 2014-08-08 14:29:09,621 main.easyconfig.templates DEBUG name: versionprefix, config: | |
| == 2014-08-08 14:29:09,621 main.MakeCp INFO Running method configure_step part of step configure | |
| == 2014-08-08 14:29:09,621 main.MakeCp INFO building... | |
| == 2014-08-08 14:29:09,622 main.MakeCp INFO Starting build step | |
| == 2014-08-08 14:29:09,624 main.easyconfig.templates DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'configure_cmd_prefix': ['', 'Prefix to be glued before ./configure', (1, 'easyblock-specific')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'prebuildopts': ['cd kmer && make install && cd .. && cd samtools && make && cd .. && cd src && ', 'Extra options pre-passed to build command.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'runtest': [None, 'Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test)', (3, 'build')], 'sources': [['wgs-%(version)s.tar.bz2'], 'List of source files', (3, 'build')], 'versionsuffix': ['', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': [None, 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'patches': [[], 'List of patches to apply', (3, 'build')], 'with_configure': [False, 'Run configure script before building', (3, 'build')], 'postinstallcmds': [[], 'Commands to run after the install step.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'start_dir': ['/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['8.1', 'Version of software', (0, 'mandatory')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'homepage': ['http://wgs-assembler.sourceforge.net/', 'The homepage of the software', (0, 'mandatory')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'tar_config_opts': [False, 'Override tar settings as determined by configure.', (1, 'easyblock-specific')], 'description': [' Celera Assembler is a de novo whole-genome shotgun (WGS) DNA \n sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary \n data produced by whole-genome shotgun sequencing. ', 'A short description of the software', (0, 'mandatory')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'source_urls': [[('http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-%(version)s/', 'download')], 'List of URLs for source files', (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'dummy': False, 'toolchain': {'version': '1.4.10', 'name': 'goolf'}, 'name': 'bzip2', 'versionsuffix': '', 'version': '1.0.6', 'mod_name': 'bzip2/1.0.6-goolf-1.4.10'}], 'List of dependencies', (5, 'dependencies')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')], 'key': [None, 'Key for installing software', (6, 'license')], 'prefix_opt': ['--prefix=', 'Prefix command line option for configure script', (1, 'easyblock-specific')], 'toolchain': [{'version': '1.4.10', 'name': 'goolf'}, 'Name and version of toolchain', (0, 'mandatory')], 'parallel': [1, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'sanity_check_paths': [{'files': ['bin/bogus', 'bin/convert-fasta-to-v2.pl', 'bin/fastqAnalyze', 'bin/markUniqueUnique', 'bin/pacBioToCA', 'bin/uidclient'], 'dirs': ['lib']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['Celera_Assembler', 'Name of software', (0, 'mandatory')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'preconfigopts': ['', 'Extra options pre-passed to configure.', (3, 'build')], 'easyblock': ['MakeCp', 'EasyBlock to use for building', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'files_to_copy': [['Linux-amd64/*'], 'List of files or dirs to copy', (0, 'mandatory')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')]} | |
| == 2014-08-08 14:29:09,627 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,627 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,628 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,628 main.easyconfig.templates DEBUG name: name, config: Celera_Assembler | |
| == 2014-08-08 14:29:09,629 main.easyconfig.templates DEBUG name: version, config: 8.1 | |
| == 2014-08-08 14:29:09,629 main.easyconfig.templates DEBUG name: versionsuffix, config: | |
| == 2014-08-08 14:29:09,630 main.easyconfig.templates DEBUG name: versionprefix, config: | |
| == 2014-08-08 14:29:09,631 main.easyconfig.templates DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'configure_cmd_prefix': ['', 'Prefix to be glued before ./configure', (1, 'easyblock-specific')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'prebuildopts': ['cd kmer && make install && cd .. && cd samtools && make && cd .. && cd src && ', 'Extra options pre-passed to build command.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'runtest': [None, 'Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test)', (3, 'build')], 'sources': [['wgs-%(version)s.tar.bz2'], 'List of source files', (3, 'build')], 'versionsuffix': ['', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': [None, 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'patches': [[], 'List of patches to apply', (3, 'build')], 'with_configure': [False, 'Run configure script before building', (3, 'build')], 'postinstallcmds': [[], 'Commands to run after the install step.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'start_dir': ['/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['8.1', 'Version of software', (0, 'mandatory')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'homepage': ['http://wgs-assembler.sourceforge.net/', 'The homepage of the software', (0, 'mandatory')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'tar_config_opts': [False, 'Override tar settings as determined by configure.', (1, 'easyblock-specific')], 'description': [' Celera Assembler is a de novo whole-genome shotgun (WGS) DNA \n sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary \n data produced by whole-genome shotgun sequencing. ', 'A short description of the software', (0, 'mandatory')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'source_urls': [[('http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-%(version)s/', 'download')], 'List of URLs for source files', (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'dummy': False, 'toolchain': {'version': '1.4.10', 'name': 'goolf'}, 'name': 'bzip2', 'versionsuffix': '', 'version': '1.0.6', 'mod_name': 'bzip2/1.0.6-goolf-1.4.10'}], 'List of dependencies', (5, 'dependencies')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')], 'key': [None, 'Key for installing software', (6, 'license')], 'prefix_opt': ['--prefix=', 'Prefix command line option for configure script', (1, 'easyblock-specific')], 'toolchain': [{'version': '1.4.10', 'name': 'goolf'}, 'Name and version of toolchain', (0, 'mandatory')], 'parallel': [1, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'sanity_check_paths': [{'files': ['bin/bogus', 'bin/convert-fasta-to-v2.pl', 'bin/fastqAnalyze', 'bin/markUniqueUnique', 'bin/pacBioToCA', 'bin/uidclient'], 'dirs': ['lib']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['Celera_Assembler', 'Name of software', (0, 'mandatory')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'preconfigopts': ['', 'Extra options pre-passed to configure.', (3, 'build')], 'easyblock': ['MakeCp', 'EasyBlock to use for building', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'files_to_copy': [['Linux-amd64/*'], 'List of files or dirs to copy', (0, 'mandatory')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')]} | |
| == 2014-08-08 14:29:09,634 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,635 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,635 main.easyconfig.templates DEBUG version found in easyconfig is 8.1 | |
| == 2014-08-08 14:29:09,636 main.easyconfig.templates DEBUG name: name, config: Celera_Assembler | |
| == 2014-08-08 14:29:09,636 main.easyconfig.templates DEBUG name: version, config: 8.1 | |
| == 2014-08-08 14:29:09,637 main.easyconfig.templates DEBUG name: versionsuffix, config: | |
| == 2014-08-08 14:29:09,637 main.easyconfig.templates DEBUG name: versionprefix, config: | |
| == 2014-08-08 14:29:09,638 main.MakeCp INFO Running method build_step part of step build | |
| == 2014-08-08 14:29:09,638 main.easyconfig.easyconfig WARNING Deprecated functionality, will no longer work in v2.0: Easyconfig parameter 'premakeopts' is deprecated, use 'prebuildopts' instead. | |
| == 2014-08-08 14:29:09,639 main.easyconfig.easyconfig WARNING Deprecated functionality, will no longer work in v2.0: Easyconfig parameter 'makeopts' is deprecated, use 'buildopts' instead. | |
| == 2014-08-08 14:29:09,639 main.run DEBUG run_cmd: running cmd . /etc/profile.d/modules.sh && cd kmer && make install && cd .. && cd samtools && make && cd .. && cd src && make -j 1 (in /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1) | |
| == 2014-08-08 14:30:36,951 main.run ERROR EasyBuild crashed with an error (at easybuild/tools/run.py:382 in parse_cmd_output): cmd ". /etc/profile.d/modules.sh && cd kmer && make install && cd .. && cd samtools && make && cd .. && cd src && make -j 1 " exited with exitcode 2 and output: | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/sfx.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/list.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/hash.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/except.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/dict.c.d | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.c | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.c: In function ‘mtRandomGaussian’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.c:166:34: warning: variable ‘y2’ set but not used [-Wunused-but-set-variable] | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar-test.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar-test.c | |
| gcc -L/usr/local/lib -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar-test /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar-test.o -pthread -ldl -lm -lbz2 | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar-test | diff - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.out > /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/diffs 2>&1 | |
| if test -s /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/diffs ; then echo 'MT19937: TEST FAILED'; else echo 'MT19937: Test Passed'; fi | |
| MT19937: Test Passed | |
| touch /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/test.c | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar-test | diff - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.out | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/test.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/sweatShop.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/speedCounter.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/recordFile.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/readBuffer.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/intervalList.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/fibonacciNumbers.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedFile.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedArray.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bigQueue.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/util.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/qsort_mt.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/palloc.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/md5.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/file.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqStream.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqCache.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/merStream.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStream.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqCache.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqFactory.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/sffFile.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStore.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaStdin.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastqFile.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaFile.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/kmer.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/reversecomplement.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/halign.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-colorspace.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-acgtspace.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet.c.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/mask.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/percentCovered.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/driver-posDB.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/driver-existDB.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-sort.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-mismatch.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-file.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-dump.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-access.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-state.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-sequence.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-meryl.C.d | |
| making /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-fasta.C.d | |
| making meryl/simple.C.d | |
| making meryl/compare-counts.C.d | |
| making meryl/maskMers.C.d | |
| making meryl/mapMers-depth.C.d | |
| making meryl/mapMers.C.d | |
| making meryl/asmMerQC.C.d | |
| making meryl/mervin.C.d | |
| making meryl/meryl.C.d | |
| making meryl/unaryOp.C.d | |
| making meryl/merge.C.d | |
| making meryl/estimate.C.d | |
| making meryl/dump.C.d | |
| making meryl/build-threads.C.d | |
| making meryl/build.C.d | |
| making meryl/binaryOp.C.d | |
| making meryl/args.C.d | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/meryl.o -c meryl/meryl.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/args.o -c meryl/args.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/binaryOp.o -c meryl/binaryOp.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build.o -c meryl/build.C | |
| meryl/build.C:248:2: warning: #warning not submitting prepareBatch to grid [-Wcpp] | |
| meryl/build.C: In function ‘void runSegment(merylArgs*, u64bit)’: | |
| meryl/build.C:426:8: warning: unused variable ‘mstring’ [-Wunused-variable] | |
| meryl/build.C: In function ‘void build(merylArgs*)’: | |
| meryl/build.C:783:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/build.C:784:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/build.C:785:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/build.C:789:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/build.C:794:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/build.C:801:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build-threads.o -c meryl/build-threads.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/dump.o -c meryl/dump.C | |
| meryl/dump.C:50:2: warning: #warning make this a test [-Wcpp] | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/estimate.o -c meryl/estimate.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/merge.o -c meryl/merge.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/unaryOp.o -c meryl/unaryOp.C | |
| rm -f meryl/libmerylguts.a && ar ruvs meryl/libmerylguts.a meryl/args.o meryl/binaryOp.o meryl/build.o meryl/build-threads.o meryl/dump.o meryl/estimate.o meryl/merge.o meryl/unaryOp.o | |
| ar: creating meryl/libmerylguts.a | |
| a - meryl/args.o | |
| a - meryl/binaryOp.o | |
| a - meryl/build.o | |
| a - meryl/build-threads.o | |
| a - meryl/dump.o | |
| a - meryl/estimate.o | |
| a - meryl/merge.o | |
| a - meryl/unaryOp.o | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C:72:2: warning: #warning not checking pmagic [-Wcpp] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C:6:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C:7:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C:8:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C:9:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C:10:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C:11:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C: In constructor ‘merylStreamReader::merylStreamReader(const char*, u32bit)’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C:42:11: warning: variable ‘Pmagic’ set but not used [-Wunused-but-set-variable] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C: In member function ‘void merylStreamWriter::addMer(u64bit, u32bit, u64bit, u32bit, u32bit, u32bit*)’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.C:469:52: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] | |
| rm -f /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a && ar ruvs /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.o | |
| ar: creating /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.o | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaFile.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaFile.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastqFile.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastqFile.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaStdin.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaStdin.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStore.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStore.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/sffFile.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/sffFile.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqFactory.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqFactory.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqCache.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqCache.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStream.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStream.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/merStream.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/merStream.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqCache.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqCache.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqStream.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqStream.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C:11:2: warning: #warning HOW DO WE TEST IF WE GET ALL THE MERS? [-Wcpp] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C: In function ‘int main(int, char**)’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C:223:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C:225:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C:228:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C:243:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C:245:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.C:248:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| rm -f /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a && ar ruvs /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaFile.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastqFile.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaStdin.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStore.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/sffFile.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqFactory.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqCache.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStream.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/merStream.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqCache.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqStream.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.o | |
| ar: creating /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaFile.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastqFile.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/fastaStdin.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStore.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/sffFile.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqFactory.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqCache.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/seqStream.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/merStream.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqCache.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqStream.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.o | |
| gcc -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet.c | |
| gcc -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-acgtspace.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-acgtspace.c | |
| gcc -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-colorspace.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-colorspace.c | |
| gcc -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/halign.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/halign.c | |
| gcc -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/reversecomplement.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/reversecomplement.c | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/kmer.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/kmer.C | |
| rm -f /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a && ar ruvs /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-acgtspace.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-colorspace.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/halign.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/reversecomplement.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/kmer.o | |
| ar: creating /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-acgtspace.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/alphabet-colorspace.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/halign.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/reversecomplement.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/kmer.o | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/file.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/file.c | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/file.c: In function ‘openFile’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/file.c:382:9: warning: variable ‘isRW’ set but not used [-Wunused-but-set-variable] | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/md5.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/md5.c | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/palloc.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/palloc.c | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/qsort_mt.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/qsort_mt.c | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/qsort_mt.c: In function ‘qsort_algo’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/qsort_mt.c:264:13: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/qsort_mt.c: In function ‘qsort_thread’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/qsort_mt.c:370:13: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/util.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/util.c | |
| g++ -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bigQueue.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bigQueue.C | |
| g++ -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedArray.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedArray.C | |
| g++ -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedFile.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedFile.C | |
| g++ -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/fibonacciNumbers.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/fibonacciNumbers.C | |
| g++ -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/intervalList.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/intervalList.C | |
| g++ -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/readBuffer.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/readBuffer.C | |
| g++ -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/recordFile.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/recordFile.C | |
| g++ -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/speedCounter.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/speedCounter.C | |
| g++ -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/sweatShop.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/sweatShop.C | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/dict.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/dict.c | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/except.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/except.c | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/hash.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/hash.c | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/list.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/list.c | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/sfx.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/sfx.c | |
| rm -f /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a && ar ruvs /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/file.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/md5.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/palloc.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/qsort_mt.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/util.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bigQueue.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedArray.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedFile.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/fibonacciNumbers.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/intervalList.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/readBuffer.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/recordFile.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/speedCounter.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/sweatShop.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/dict.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/except.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/hash.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/list.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/sfx.o | |
| ar: creating /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/file.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/md5.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/palloc.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/qsort_mt.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/util.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bigQueue.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedArray.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/bitPackedFile.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/fibonacciNumbers.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/intervalList.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/readBuffer.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/recordFile.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/speedCounter.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/sweatShop.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/dict.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/except.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/hash.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/list.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/sfx.o | |
| g++ -L/usr/local/lib -o meryl/meryl meryl/meryl.o meryl/libmerylguts.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mervin.o -c meryl/mervin.C | |
| meryl/mervin.C: In member function ‘void kmerSorter::merge(u64bit*, u32bit)’: | |
| meryl/mervin.C:200:10: warning: variable ‘broken’ set but not used [-Wunused-but-set-variable] | |
| g++ -L/usr/local/lib -o meryl/mervin meryl/mervin.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/simple.o -c meryl/simple.C | |
| g++ -L/usr/local/lib -o meryl/simple meryl/simple.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/asmMerQC.o -c meryl/asmMerQC.C | |
| meryl/asmMerQC.C: In function ‘void compare(merylStreamReader*, merylStreamReader*, kMer&, u32bit, u32bit (*)[6])’: | |
| meryl/asmMerQC.C:111:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses] | |
| meryl/asmMerQC.C:130:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses] | |
| meryl/asmMerQC.C:149:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses] | |
| meryl/asmMerQC.C: In function ‘int main(int, char**)’: | |
| meryl/asmMerQC.C:384:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/asmMerQC.C:385:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/asmMerQC.C:386:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/asmMerQC.C:387:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/asmMerQC.C:388:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/asmMerQC.C:389:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| g++ -L/usr/local/lib -o meryl/asmMerQC meryl/asmMerQC.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers.o -c meryl/mapMers.C | |
| meryl/mapMers.C: In function ‘int main(int, char**)’: | |
| meryl/mapMers.C:21:13: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-fasta.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-fasta.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-meryl.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-meryl.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-sequence.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-sequence.C | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-sequence.C: In member function ‘bool existDB::createFromSequence(const char*, u32bit, u32bit)’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-sequence.C:41:70: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat] | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-state.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-state.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-access.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-access.C | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-access.C: In member function ‘void positionDB::filter(u64bit, u64bit)’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-access.C:204:11: warning: unused variable ‘vv’ [-Wunused-variable] | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-dump.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-dump.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-file.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-file.C | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-file.C: In member function ‘void positionDB::saveState(const char*)’: | |
| /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-file.C:63:73: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-mismatch.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-mismatch.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-sort.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-sort.C | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB.C | |
| rm -f /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a && ar ruvs /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-fasta.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-meryl.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-sequence.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-state.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-access.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-dump.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-file.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-mismatch.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-sort.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB.o | |
| ar: creating /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-fasta.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-meryl.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-create-from-sequence.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB-state.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-access.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-dump.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-file.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-mismatch.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB-sort.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB.o | |
| g++ -L/usr/local/lib -o meryl/mapMers meryl/mapMers.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers-depth.o -c meryl/mapMers-depth.C | |
| meryl/mapMers-depth.C: In function ‘int main(int, char**)’: | |
| meryl/mapMers-depth.C:17:13: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] | |
| g++ -L/usr/local/lib -o meryl/mapMers-depth meryl/mapMers-depth.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/testPositionBias.o -c meryl/testPositionBias.C | |
| meryl/testPositionBias.C: In function ‘void showBias(u32bit)’: | |
| meryl/testPositionBias.C:54:43: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/testPositionBias.C:55:50: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/testPositionBias.C:56:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/testPositionBias.C: In function ‘double computeRMSD(u32bit)’: | |
| meryl/testPositionBias.C:83:43: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/testPositionBias.C:84:50: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| meryl/testPositionBias.C:85:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| g++ -L/usr/local/lib -o meryl/testPositionBias meryl/testPositionBias.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/maskMers.o -c meryl/maskMers.C | |
| g++ -L/usr/local/lib -o meryl/maskMers meryl/maskMers.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/compare-counts.o -c meryl/compare-counts.C | |
| g++ -L/usr/local/lib -o meryl/compare-counts meryl/compare-counts.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/driver-existDB.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/driver-existDB.C | |
| g++ -L/usr/local/lib -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/existDB /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/driver-existDB.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/driver-posDB.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/driver-posDB.C | |
| g++ -L/usr/local/lib -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/positionDB /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/driver-posDB.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/percentCovered.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/percentCovered.C | |
| g++ -L/usr/local/lib -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/percentCovered /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/percentCovered.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -O2 -march=native -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/ -I/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/ -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/mask.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/mask.C | |
| g++ -L/usr/local/lib -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/mask /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/mask.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libkmer/libkmer.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libmeryl/libmeryl.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -L/usr/local/lib -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqCache /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqCache.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -L/usr/local/lib -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqStream /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-seqStream.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| g++ -L/usr/local/lib -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/test-merStream.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libseq/libseq.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libbio/libbio.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 | |
| gcc -O2 -march=native -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/test.o -c /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/test.c | |
| rm -f /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/libmt19937ar.a && ar ruvs /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/libmt19937ar.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/test.o | |
| ar: creating /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/libmt19937ar.a | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/mt19937ar.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/mt19937ar/test.o | |
| rm -f /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/libkaz.a && ar ruvs /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/libkaz.a /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/dict.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/except.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/hash.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/list.o /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/sfx.o | |
| ar: creating /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/libkaz.a | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/dict.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/except.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/hash.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/list.o | |
| a - /home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/kmer/libutil/kazlib/sfx.o | |
| make[1]: Entering directory `/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/samtools-0.1.19' | |
| make[2]: Entering directory `/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/samtools-0.1.19' | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o | |
| bgzf.c: In function ‘worker_aux’: | |
| bgzf.c:392:9: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] | |
| bgzf.c: In function ‘bgzf_close’: | |
| bgzf.c:572:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o | |
| bam_pileup.c: In function ‘resolve_cigar2’: | |
| bam_pileup.c:75:9: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable] | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o | |
| bam_reheader.c: In function ‘bam_reheader’: | |
| bam_reheader.c:12:16: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o | |
| kprobaln.c: In function ‘kpa_glocal’: | |
| kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o | |
| ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o | |
| make[2]: Leaving directory `/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/samtools-0.1.19' | |
| make[2]: Entering directory `/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/samtools-0.1.19/bcftools' | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o | |
| bcf.c: In function ‘bcf_fmt_core’: | |
| bcf.c:233:9: warning: variable ‘iPL’ set but not used [-Wunused-but-set-variable] | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o | |
| bcfutils.c: In function ‘bcf_fit_alt’: | |
| bcfutils.c:119:9: warning: variable ‘ipl’ set but not used [-Wunused-but-set-variable] | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o | |
| em.c: In function ‘bcf_em1’: | |
| em.c:174:12: warning: variable ‘n2’ set but not used [-Wunused-but-set-variable] | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o | |
| ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o | |
| make[2]: Leaving directory `/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/samtools-0.1.19/bcftools' | |
| make[2]: Entering directory `/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/samtools-0.1.19/misc' | |
| make[2]: Nothing to be done for `lib'. | |
| make[2]: Leaving directory `/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/samtools-0.1.19/misc' | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o | |
| cut_target.c: In function ‘main_cut_target’: | |
| cut_target.c:137:36: warning: variable ‘lastpos’ set but not used [-Wunused-but-set-variable] | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o | |
| gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o | |
| gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/GCC/4.7.2/lib64 -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/GCC/4.7.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/FFTW/3.3.3-gompi-1.4.10/lib -L/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/bzip2/1.0.6-goolf-1.4.10/lib libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread | |
| /usr/bin/ld: cannot find -lcurses | |
| collect2: error: ld returned 1 exit status | |
| make[1]: *** [samtools] Error 1 | |
| make[1]: Leaving directory `/home/GMI/petar.forai/.local/easybuild/build/Celera_Assembler/8.1/goolf-1.4.10/wgs-8.1/samtools-0.1.19' | |
| make: *** [all-recur] Error 1 | |
| == 2014-08-08 14:30:36,953 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 ". /etc/profile.d/modules.sh && cd kmer && make install && cd .. && cd samtools && make && cd .. && cd src && make -j 1 " exited with exitcode 2 and output: | |
| making /home/GMI/petar.forai/.local/easybuild/build/C | |
| == 2014-08-08 14:30:36,953 main.MakeCp INFO Closing log for application name Celera_Assembler version 8.1 |
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Samtools needs a little patch (same patch that is in EB already) to look for ncurses instead of curses.