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Created February 3, 2022 22:15
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rvtests-log
== 2022-02-03 22:14:01,848 easyblock.py:295 INFO This is EasyBuild 4.5.0-rce21bd8758bda3e28ace9d4e3c7527e50077cd81 (framework: 4.5.0-rbe97b6553afcefae7f1731e6e0e75462bb032218, easyblocks: 4.5.0-rce21bd8758bda3e28ace9d4e3c7527e50077cd81) on host build-node.computecanada.ca.
== 2022-02-03 22:14:01,848 easyblock.py:301 INFO This is easyblock MakeCp from module easybuild.easyblocks.generic.makecp (/cvmfs/soft.computecanada.ca/easybuild/site-packages/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py)
== 2022-02-03 22:14:01,849 easyblock.py:971 INFO Build dir set to /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0
== 2022-02-03 22:14:01,850 easyblock.py:1031 INFO Software install dir set to /home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0
== 2022-02-03 22:14:01,850 easyblock.py:1036 INFO Module install dir set to /home/mboisson/.local/easybuild/modules/2020/
== 2022-02-03 22:14:01,850 easyblock.py:280 INFO Init completed for application name rvtests version 2.1.0
== 2022-02-03 22:14:01,850 easyblock.py:3937 INFO Obtained application instance of for rvtests (easyblock: MakeCp)
== 2022-02-03 22:14:01,850 easyconfig.py:1686 INFO Generating template values...
== 2022-02-03 22:14:01,851 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-02-03 22:14:01,852 one.py:175 INFO Skipping reformatting value for parameter 'toolchain'
== 2022-02-03 22:14:01,852 filetools.py:1870 INFO Creating directory /tmp/eb-7_4x5zsi/reprod_20220203221401_16100 (parents: True, set_gid: False, sticky: False)
== 2022-02-03 22:14:01,853 easyblock.py:4183 INFO Dumped easyconfig instance to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/rvtests-2.1.0-GCCcore-9.3.0.eb
== 2022-02-03 22:14:01,853 filetools.py:1870 INFO Creating directory /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks (parents: True, set_gid: False, sticky: False)
== 2022-02-03 22:14:01,853 filetools.py:2383 INFO /cvmfs/soft.computecanada.ca/easybuild/site-packages/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks/configuremake.py
== 2022-02-03 22:14:01,854 easyblock.py:4163 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks
== 2022-02-03 22:14:01,855 filetools.py:2383 INFO /cvmfs/soft.computecanada.ca/easybuild/site-packages/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py copied to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks/makecp.py
== 2022-02-03 22:14:01,856 easyblock.py:4163 INFO Dumped easyblock makecp.py required for reproduction to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks
== 2022-02-03 22:14:01,856 filetools.py:1870 INFO Creating directory /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/hooks (parents: True, set_gid: False, sticky: False)
== 2022-02-03 22:14:01,856 filetools.py:2383 INFO /cvmfs/soft.computecanada.ca/easybuild/cc_hooks_gentoo.py copied to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/hooks/cc_hooks_gentoo.py
== 2022-02-03 22:14:01,856 easyblock.py:4195 INFO Dumped hooks file /cvmfs/soft.computecanada.ca/easybuild/cc_hooks_gentoo.py which is (potentially) required for reproduction to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/hooks/cc_hooks_gentoo.py
== 2022-02-03 22:14:01,857 easyblock.py:2018 INFO Number of iterations to perform for central part of installation procedure: 1
== 2022-02-03 22:14:01,857 build_log.py:266 INFO building and installing avx2/Core/rvtests/2.1.0...
== 2022-02-03 22:14:01,862 filetools.py:1963 INFO Lock /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock does not exist
== 2022-02-03 22:14:01,862 filetools.py:1904 INFO Creating lock at /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock...
== 2022-02-03 22:14:01,862 filetools.py:1870 INFO Creating directory /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock (parents: True, set_gid: False, sticky: False)
== 2022-02-03 22:14:01,863 filetools.py:1913 INFO Lock created: /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock
== 2022-02-03 22:14:01,863 build_log.py:266 INFO fetching files...
== 2022-02-03 22:14:01,865 easyblock.py:3648 INFO Starting fetch step
== 2022-02-03 22:14:01,865 easyconfig.py:1686 INFO Generating template values...
== 2022-02-03 22:14:01,865 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-02-03 22:14:01,865 hooks.py:166 INFO Found pre_fetch_hook hook
== 2022-02-03 22:14:01,866 hooks.py:198 INFO Running 'pre_fetch_hook' hook function (arguments: [<easybuild.easyblocks.generic.makecp.MakeCp object at 0x2adbdf81fb10>])...
== 2022-02-03 22:14:01,866 easyblock.py:3656 INFO Running method fetch_step part of step fetch
== 2022-02-03 22:14:01,866 easyblock.py:2140 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2022-02-03 22:14:01,866 tools.py:271 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /cvmfs/soft.computecanada.ca/easybuild/framework/eb
== 2022-02-03 22:14:01,866 tools.py:287 INFO Not considering /cvmfs/soft.computecanada.ca/easybuild (no easybuild/easyconfigs subdir found)
== 2022-02-03 22:14:01,866 tools.py:295 INFO Also considering installation prefix /cvmfs/soft.computecanada.ca/easybuild/site-packages (via resolved path to 'eb')...
== 2022-02-03 22:14:01,867 easyblock.py:788 INFO Found file checksums.json at /home/mboisson/git/easybuild-easyconfigs/easybuild/easyconfigs/r/rvtests/checksums.json
== 2022-02-03 22:14:01,867 easyblock.py:377 INFO Loading checksums from file /home/mboisson/git/easybuild-easyconfigs/easybuild/easyconfigs/r/rvtests/checksums.json
== 2022-02-03 22:14:01,868 tools.py:271 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /cvmfs/soft.computecanada.ca/easybuild/framework/eb
== 2022-02-03 22:14:01,868 tools.py:287 INFO Not considering /cvmfs/soft.computecanada.ca/easybuild (no easybuild/easyconfigs subdir found)
== 2022-02-03 22:14:01,868 tools.py:295 INFO Also considering installation prefix /cvmfs/soft.computecanada.ca/easybuild/site-packages (via resolved path to 'eb')...
== 2022-02-03 22:14:01,869 easyblock.py:788 INFO Found file v2.1.0.tar.gz at /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz
== 2022-02-03 22:14:01,869 easyblock.py:470 INFO Added sources: [{'name': 'v2.1.0.tar.gz', 'path': '/home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz', 'cmd': None, 'checksum': 'bc05cd1ab1cbeda62bd79fd3ba0f46b8e304a1bc1bea556316baa2c38ef1fcf3', 'finalpath': '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0'}]
== 2022-02-03 22:14:01,869 easyblock.py:2183 INFO no patches provided
== 2022-02-03 22:14:01,931 easyblock.py:2193 INFO md5 checksum for /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz: 4a671a2ae942458bf2494e6c2f96408f
== 2022-02-03 22:14:01,995 easyblock.py:2193 INFO sha256 checksum for /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz: bc05cd1ab1cbeda62bd79fd3ba0f46b8e304a1bc1bea556316baa2c38ef1fcf3
== 2022-02-03 22:14:01,996 easyblock.py:2228 INFO Checking dirs that need to be created: ['/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', '/home/mboisson/.local/easybuild/modules/2020/avx2/Core/rvtests']
== 2022-02-03 22:14:01,997 configuremake.py:94 INFO config.guess version: 2018-08-29 (last updated: 2022-02-02T14:30:45.237457, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c)
== 2022-02-03 22:14:01,997 configuremake.py:149 INFO Found config.guess at /home/mboisson/.local/easybuild/sources/generic/eb_v4.5.0/ConfigureMake/config.guess
== 2022-02-03 22:14:01,997 build_log.py:266 INFO creating build dir, resetting environment...
== 2022-02-03 22:14:02,000 easyblock.py:3648 INFO Starting ready step
== 2022-02-03 22:14:02,000 easyconfig.py:1686 INFO Generating template values...
== 2022-02-03 22:14:02,000 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-02-03 22:14:02,001 easyblock.py:3656 INFO Running method check_readiness_step part of step ready
== 2022-02-03 22:14:02,001 easyblock.py:2037 INFO Setting parallelism: 8
== 2022-02-03 22:14:02,048 easyblock.py:2089 WARNING Loaded modules detected: ['gentoo/2020']
== 2022-02-03 22:14:02,049 easyblock.py:3656 INFO Running method make_builddir part of step ready
== 2022-02-03 22:14:02,049 easyblock.py:1056 INFO Found old directory /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0
== 2022-02-03 22:14:02,189 filetools.py:380 INFO Path /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0 successfully removed.
== 2022-02-03 22:14:02,190 easyblock.py:1064 INFO Removed old directory /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0
== 2022-02-03 22:14:02,190 filetools.py:1870 INFO Creating directory /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0 (parents: True, set_gid: False, sticky: False)
== 2022-02-03 22:14:02,190 easyblock.py:3656 INFO Running method reset_env part of step ready
== 2022-02-03 22:14:02,191 easyblock.py:3656 INFO Running method handle_iterate_opts part of step ready
== 2022-02-03 22:14:02,191 easyconfig.py:1686 INFO Generating template values...
== 2022-02-03 22:14:02,191 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-02-03 22:14:02,192 build_log.py:266 INFO unpacking...
== 2022-02-03 22:14:02,195 easyblock.py:3648 INFO Starting source step
== 2022-02-03 22:14:02,195 easyconfig.py:1686 INFO Generating template values...
== 2022-02-03 22:14:02,195 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-02-03 22:14:02,195 easyblock.py:3656 INFO Running method checksum_step part of step source
== 2022-02-03 22:14:02,285 easyblock.py:2246 INFO Checksum verification for /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz using bc05cd1ab1cbeda62bd79fd3ba0f46b8e304a1bc1bea556316baa2c38ef1fcf3 passed.
== 2022-02-03 22:14:02,286 easyblock.py:3656 INFO Running method extract_step part of step source
== 2022-02-03 22:14:02,286 easyblock.py:2349 INFO Unpacking source v2.1.0.tar.gz
== 2022-02-03 22:14:02,287 run.py:233 INFO running cmd: tar xzf /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz
== 2022-02-03 22:14:02,562 build_log.py:266 INFO patching...
== 2022-02-03 22:14:02,565 easyblock.py:3648 INFO Starting patch step
== 2022-02-03 22:14:02,565 easyconfig.py:1686 INFO Generating template values...
== 2022-02-03 22:14:02,565 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-02-03 22:14:02,565 easyblock.py:3656 INFO Running method patch_step part of step patch
== 2022-02-03 22:14:02,565 build_log.py:266 INFO preparing...
== 2022-02-03 22:14:02,568 easyblock.py:3648 INFO Starting prepare step
== 2022-02-03 22:14:02,568 easyconfig.py:1686 INFO Generating template values...
== 2022-02-03 22:14:02,568 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-02-03 22:14:02,568 hooks.py:166 INFO Found pre_prepare_hook hook
== 2022-02-03 22:14:02,568 hooks.py:198 INFO Running 'pre_prepare_hook' hook function (arguments: [<easybuild.easyblocks.generic.makecp.MakeCp object at 0x2adbdf81fb10>])...
== 2022-02-03 22:14:02,568 environment.py:91 INFO Environment variable EBROOTLIBXML2 set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,568 environment.py:91 INFO Environment variable EBROOTLIBJPEGMINTURBO set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTLIBPNG set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTLIBTIFF set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTZLIB set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTLIBGLU set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTMESA set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTFLTK set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTTCL set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTTK set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTBZIP2 set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTZSTD set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTFREETYPE set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTGLIB set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBROOTSZIP set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBROOTLIBXMLPLUSPLUS set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBROOTSQLITE3 set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBROOTLIBEVENT set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined)
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBVERSIONTCL set to 8.6 (previously undefined)
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBVERSIONTK set to 8.6 (previously undefined)
== 2022-02-03 22:14:02,570 easyblock.py:3656 INFO Running method prepare_step part of step prepare
== 2022-02-03 22:14:02,571 environment.py:91 INFO Environment variable PKG_CONFIG_PATH set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr/lib/pkgconfig (previously undefined)
== 2022-02-03 22:14:03,511 modules.py:626 INFO Checking whether Core/gcccore/.9.3.0 exists...
== 2022-02-03 22:14:03,511 modules.py:638 INFO Checking whether hidden module Core/gcccore/.9.3.0 exists via 'show'...
== 2022-02-03 22:14:04,197 modules.py:654 INFO Result for existence check of Core/gcccore/.9.3.0 module: True
== 2022-02-03 22:14:05,062 modules.py:626 INFO Checking whether gcccore/.9.3.0 exists...
== 2022-02-03 22:14:05,062 modules.py:638 INFO Checking whether hidden module gcccore/.9.3.0 exists via 'show'...
== 2022-02-03 22:14:05,752 modules.py:654 INFO Result for existence check of gcccore/.9.3.0 module: True
== 2022-02-03 22:14:05,753 toolchain.py:760 INFO List of toolchain dependency modules and toolchain definition match!
== 2022-02-03 22:14:05,755 compiler.py:361 INFO _set_optimal_architecture: using march=core-avx2 as optarch for x86_64.
== 2022-02-03 22:14:05,757 environment.py:91 INFO Environment variable CC set to gcc (previously undefined)
== 2022-02-03 22:14:05,757 environment.py:91 INFO Environment variable EBVARCC set to gcc (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable CXX set to g++ (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARCXX set to g++ (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable F77 set to gfortran (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARF77 set to gfortran (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable F90 set to gfortran (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARF90 set to gfortran (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable FC set to gfortran (previously undefined)
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARFC set to gfortran (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable FLIBS set to -lgfortran (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable LDFLAGS set to -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARLDFLAGS set to -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable LIBS set to -lm -lpthread (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=core-avx2 (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=core-avx2 (previously undefined)
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,760 environment.py:91 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined)
== 2022-02-03 22:14:05,760 toolchain.py:910 INFO Using ccache for these compiler commands: gcc, g++
== 2022-02-03 22:14:05,760 environment.py:91 INFO Environment variable CCACHE_DIR set to /cvmfs/local/ccache (previously undefined)
== 2022-02-03 22:14:05,760 environment.py:91 INFO Environment variable CCACHE_TEMPDIR set to /tmp/eb-7_4x5zsi/tmpxetixyh3 (previously undefined)
== 2022-02-03 22:14:05,760 filetools.py:520 INFO Command ccache found at /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/ccache
== 2022-02-03 22:14:05,760 environment.py:91 INFO Environment variable PATH set to /tmp/eb-7_4x5zsi/tmpip3lj4zh:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/bin (previous value: '/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/bin')
== 2022-02-03 22:14:05,761 filetools.py:520 INFO Command gcc found at /tmp/eb-7_4x5zsi/tmpip3lj4zh/gcc
== 2022-02-03 22:14:05,761 filetools.py:520 INFO Command g++ found at /tmp/eb-7_4x5zsi/tmpip3lj4zh/g++
== 2022-02-03 22:14:05,761 toolchain.py:789 INFO Commands symlinked to /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/ccache via /tmp/eb-7_4x5zsi/tmpip3lj4zh: gcc, g++
== 2022-02-03 22:14:05,761 easyblock.py:1921 INFO Using /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/ as start dir
== 2022-02-03 22:14:05,761 hooks.py:166 INFO Found post_prepare_hook hook
== 2022-02-03 22:14:05,762 hooks.py:198 INFO Running 'post_prepare_hook' hook function (arguments: [<easybuild.easyblocks.generic.makecp.MakeCp object at 0x2adbdf81fb10>])...
== 2022-02-03 22:14:05,762 build_log.py:266 INFO ... (took 3 secs)
== 2022-02-03 22:14:05,764 build_log.py:266 INFO configuring...
== 2022-02-03 22:14:05,767 easyblock.py:3648 INFO Starting configure step
== 2022-02-03 22:14:05,767 easyconfig.py:1686 INFO Generating template values...
== 2022-02-03 22:14:05,767 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-02-03 22:14:05,768 hooks.py:166 INFO Found pre_configure_hook hook
== 2022-02-03 22:14:05,768 hooks.py:198 INFO Running 'pre_configure_hook' hook function (arguments: [<easybuild.easyblocks.generic.makecp.MakeCp object at 0x2adbdf81fb10>])...
== 2022-02-03 22:14:05,768 easyconfig.py:1892 INFO Derived full easyblock module path for MakeCp: easybuild.easyblocks.generic.makecp
== 2022-02-03 22:14:05,768 easyconfig.py:1939 INFO Successfully obtained class 'MakeCp' for easyblock 'MakeCp' (software name 'rvtests')
== 2022-02-03 22:14:05,768 easyblock.py:3656 INFO Running method configure_step part of step configure
== 2022-02-03 22:14:05,768 build_log.py:266 INFO building...
== 2022-02-03 22:14:05,770 easyblock.py:3648 INFO Starting build step
== 2022-02-03 22:14:05,770 easyconfig.py:1686 INFO Generating template values...
== 2022-02-03 22:14:05,771 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-02-03 22:14:05,771 easyblock.py:3656 INFO Running method build_step part of step build
== 2022-02-03 22:14:05,771 configuremake.py:338 INFO Building target ''
== 2022-02-03 22:14:05,771 run.py:233 INFO running cmd: make -j 8
== 2022-02-03 22:14:17,738 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/site-packages/easybuild-framework/easybuild/base/exceptions.py:124 in __init__): cmd " make -j 8 " exited with exit code 2 and output:
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third cnpy
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third zstd
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
unzip -o cnpy.zip ## -o: overwrite existing file
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third sqlite
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
echo "obtain zstd"
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third nlopt
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
obtain zstd
echo "obtain sqlite"
wget --no-check-certificate https://github.com/facebook/zstd/archive/v1.3.1.tar.gz -O zstd-1.3.1.tar.gz
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third bzip2
Archive: cnpy.zip
b39d58d3640f77c043bfe92591afeafdd82e78db
creating: cnpy-master/
inflating: cnpy-master/CMakeLists.txt
inflating: cnpy-master/LICENSE
inflating: cnpy-master/README
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
inflating: cnpy-master/cnpy.cpp
inflating: cnpy-master/cnpy.h
inflating: cnpy-master/example1.cpp
inflating: cnpy-master/mat2npz
inflating: cnpy-master/npy2mat
inflating: cnpy-master/npz2mat
ln -s -f cnpy-master cnpy
obtain sqlite
wget --no-check-certificate https://sqlite.org/2017/sqlite-autoconf-3200100.tar.gz
--2022-02-03 22:14:05-- https://github.com/facebook/zstd/archive/v1.3.1.tar.gz
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third zlib
(cd cnpy; g++ -std=c++11 -c cnpy.cpp; ar rcs libcnpy.a cnpy.o)
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
tar zxf nlopt-2.4.2.tar.gz
--2022-02-03 22:14:05-- https://sqlite.org/2017/sqlite-autoconf-3200100.tar.gz
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third gsl
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
tar zxf bzip2-1.0.6.tar.gz
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third pcre
tar zxf zlib-1.2.8.tar.gz
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
tar zxf gsl-1.16.tar.gz
Resolving github.com... mv pcre-8.36.tar.gz* pcre-8.36.tar.gz
Resolving sqlite.org... 140.82.114.3
Connecting to github.com|140.82.114.3|:443... mv: 'pcre-8.36.tar.gz' and 'pcre-8.36.tar.gz' are the same file
make[1]: [Makefile:14: pcre] Error 1 (ignored)
tar zxf pcre-8.36.tar.gz
(DIR=`pwd`; cd nlopt-2.4.2; ./configure --prefix="${DIR}"/nlopt; make -j; make install)
(DIR=`pwd`; cd pcre-8.36; ./configure --prefix="${DIR}"/pcre; make -j; make install)
ln -s -f zlib-1.2.8 zlib
(cd zlib; ./configure; make)
connected.
45.33.6.223, 2600:3c00::f03c:91ff:fe96:b959
Connecting to sqlite.org|45.33.6.223|:443... ln -s -f bzip2-1.0.6 bzip2
(cd bzip2-1.0.6; make)
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/bzip2-1.0.6'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
If compilation produces errors, or a large number of warnings,
please read README.COMPILATION.PROBLEMS -- you might be able to
adjust the flags in this Makefile to improve matters.
Also in README.COMPILATION.PROBLEMS are some hints that may help
if your build produces an executable which is unable to correctly
handle so-called 'large files' -- files of size 2GB or more.
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c
checking for a BSD-compatible install... /cvmfs/soft.computecanada.ca/custom/bin/install -c
checking whether build environment is sane... yes
(DIR=`pwd`; cd gsl-1.16; ./configure --prefix="${DIR}"/gsl; make -j; make install)
HTTP request sent, awaiting response... checking for a thread-safe mkdir -p... /cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
connected.
checking whether make supports nested variables... checking for a BSD-compatible install... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for gcc... gcc
/cvmfs/soft.computecanada.ca/custom/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking for a BSD-compatible install... /cvmfs/soft.computecanada.ca/custom/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for a sed that does not truncate output... /cvmfs/soft.computecanada.ca/gentoo/2020/bin/sed
HTTP request sent, awaiting response... checking whether make sets $(MAKE)... (cached) yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
302 Found
Location: https://codeload.github.com/facebook/zstd/tar.gz/v1.3.1 [following]
--2022-02-03 22:14:06-- https://codeload.github.com/facebook/zstd/tar.gz/v1.3.1
Resolving codeload.github.com... 140.82.113.9
Connecting to codeload.github.com|140.82.113.9|:443... make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third pcre
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
mv pcre-8.36.tar.gz* pcre-8.36.tar.gz
mv: 'pcre-8.36.tar.gz' and 'pcre-8.36.tar.gz' are the same file
make[1]: [Makefile:14: pcre] Error 1 (ignored)
tar zxf pcre-8.36.tar.gz
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c
200 OK
Length: 2565638 (2.4M) [application/x-gzip]
Saving to: sqlite-autoconf-3200100.tar.gz
connected.
(DIR=`pwd`; cd pcre-8.36; ./configure --prefix="${DIR}"/pcre; make -j; make install)
0K .......... .......... .......... ..HTTP request sent, awaiting response... ........ .......... 1% 408K 6s
50K .......... .......... ..........checking for a BSD-compatible install... /cvmfs/soft.computecanada.ca/custom/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... .......... ....../cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
.... 3% 817K 4s
100K .......... .......... .......... .......... .......... 5% 58.3M 3s
150K .......... .......... ......checking whether make supports nested variables... (cached) yes
.... .......... ..checking for style of include used by make... GNU
checking for gcc... gcc
........ 7% 1.29M 3s
200K ........gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c
.. .......... .......... .......... .......... 9% 1.91M 2s
250K .......... .......... .......... .......... .......... 11% 218M 2s
300K .......... .......... .......... .......... .......... 13% 212M 2s
350K .......... .......... ...checking whether the C compiler works... ....... .......... .......... 15% 13.2M 1sno
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2':
configure: error: C compiler cannot create executables
See `config.log' for more details
400K .......... .......... .......... .......... ........make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: *** No targets specified and no makefile found. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2'
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[2]: *** No rule to make target 'install'. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2'
make[1]: [Makefile:46: nlopt] Error 2 (ignored)
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third tabix
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
mv tabix-0.2.6.tar.bz2* tabix-0.2.6.tar.bz2
mv: 'tabix-0.2.6.tar.bz2' and 'tabix-0.2.6.tar.bz2' are the same file
make[1]: [Makefile:7: tabix] Error 1 (ignored)
tar jxf tabix-0.2.6.tar.bz2
checking whether the C compiler works... 200 OK
Length: unspecified [application/x-gzip]
Saving to: zstd-1.3.1.tar.gz
0K .......... .... 17% 854K 1s
450K .......... .......... .......... .......... .......... 19% 61.6M 1s
500K .......... .......... .......... .......... .......... 21% 134M 1s
550K .......... .......... .......... .......... .......... 23% 94.0M 1s
600K .......... .......... .......... .......... .......... 25% 144M 1s
650K .......... .......... .......... .......... .......... 27% 199M 1s
700K .......... .......... .......... .......... .......... 29% 65.7M 1s
750K .......... .......... .......... .......... .......... 31% 175M 1s
800K .......... ......no
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16':
configure: error: C compiler cannot create executables
See `config.log' for more details
Checking for shared library support...
.... .......... .......... .......... 33% 1.51M 1s
850K .......... .......... .......... .......... .......... 35% 183M 1s
900K .......... ..make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: *** No targets specified and no makefile found. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16'
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[2]: *** No rule to make target 'install'. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16'
make[1]: [Makefile:20: gsl] Error 2 (ignored)
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third samtools
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
checking whether the C compiler works... tar jxf samtools-0.1.19.tar.bz2
........ .......... .......... .......... 37% 1.87M 1s
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1650K .......... ....no
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36':
configure: error: C compiler cannot create executables
See `config.log' for more details
...... .......... .......... .......... 67% 1.70M 0s
1700K .......... .......... .......... .......... .......... 69% 201M 0s
1750K .......... .......... .......... .......... .......... 71% 228M 0s
1800K .......... .......... ....make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: *** No targets specified and no makefile found. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36'
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[2]: *** No rule to make target 'install'. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36'
make[1]: [Makefile:16: pcre] Error 2 (ignored)
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third samtools
ln -s -f tabix-0.2.6 tabix
sed -i.bak 's:^CFLAGS=:CFLAGS=-I../zlib-1.2.8:;s:^LIBPATH=:LIBPATH=-L../zlib-1.2.8:' tabix/Makefile
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
(cd tabix-0.2.6; make)
tar jxf samtools-0.1.19.tar.bz2
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/tabix-0.2.6'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
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1950K .......... .......... .......... ....gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c
...... .......... 79% 54.1M 0s
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2150K .......... ...make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/tabix-0.2.6'
..gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bgzf.c -o bgzf.o
..... .......... .......... .......... 87% 238M 0s
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2400K .......... .......... .......... .......... .......... 97% 189M 0s
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2500K ..... 100% 193M=0.4s
2022-02-03 22:14:06 (5.59 MB/s) - sqlite-autoconf-3200100.tar.gz saved [2565638/2565638]
tar zxf sqlite-autoconf-3200100.tar.gz
.......... 380K
50K .......... .......... .......... .......... ...Building shared library libz.so.1.2.8 with gcc.
ln -s -f samtools-0.1.19 samtools
sed -i.bak 's:^CFLAGS=:CFLAGS=-I../zlib-1.2.8 -I../../zlib-1.2.8:;s:^LIBPATH=:LIBPATH=-L../zlib-1.2.8 -L../../zlib-1.2.8:' samtools/Makefile samtools/bcftools/Makefile
(cd samtools; make lib-recur)
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19'
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c
ln -s -f samtools-0.1.19 samtools
sed -i.bak 's:^CFLAGS=:CFLAGS=-I../zlib-1.2.8 -I../../zlib-1.2.8:;s:^LIBPATH=:LIBPATH=-L../zlib-1.2.8 -L../../zlib-1.2.8:' samtools/Makefile samtools/bcftools/Makefile
(cd samtools; make lib-recur)
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
....... 736K
100K .......... .......... .......... .......... .......... 76.5M
150K .......... .......... .......... .......... .......... 81.9M
200K ..make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19'
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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
(DIR=`pwd`; cd sqlite-autoconf-3200100; ./configure --prefix="${DIR}"/sqlite --enable-dynamic-extensions=no; make -j; make install)
........ ......bgzf.c: In function worker_aux:
bgzf.c:392:9: warning: variable tmp set but not used [-Wunused-but-set-variable]
392 | int i, tmp, stop = 0;
| ^~~
bgzf.c: In function bgzf_close:
bgzf.c:572:11: warning: variable count set but not used [-Wunused-but-set-variable]
572 | int ret, count, block_length;
| ^~~~~
bgzf.c: In function worker_aux:
bgzf.c:392:9: warning: variable tmp set but not used [-Wunused-but-set-variable]
392 | int i, tmp, stop = 0;
| ^~~
bgzf.c: In function bgzf_close:
bgzf.c:572:11: warning: variable count set but not used [-Wunused-but-set-variable]
572 | int ret, count, block_length;
| ^~~~~
.... .......... .......... .......... 769K
250K .......... .......... .......... .......... .......... 78.2M
300K ..........gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
bgzf.c: In function bgzf_close:
bgzf.c:435:11: warning: variable count set but not used [-Wunused-but-set-variable]
435 | int ret, count, block_length;
| ^~~~~
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE kstring.c -o kstring.o
Checking for off64_t... Yes.
Checking for fseeko... Yes.
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
.......... .......... .......... .......... 792K
350K .......... .......... .......... .......... .......... 25.1M
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500K .......... .......... .......... .......... .......... 199M
550K .......... .......... .......... .......... .......... 131M
600K .......gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE knetfile.c -o knetfile.o
checking for a BSD-compatible install... gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c
/cvmfs/soft.computecanada.ca/custom/bin/install -c
checking whether build environment is sane... yes
Checking for strerror... Yes.
checking for a thread-safe mkdir -p... ... .......... .......... .......... .......... 791K
650K .......... .......... .......... .......... .......... 177M
700K .......... .......... .......... .......... .......... 213M
750K .......... .......... .......... .../cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p
....... .........checking for gawk... . 91.8M
800K .......... .....gawk
checking whether make sets $(MAKE)... ..... .......... .......... .......... 78.9M
850K .......... .......... .......... .......... .......... 238M
900K .......... .......... .......... .......... .......... 165M
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1100K .......... .......... .......... .......... .......... 240M
1150K .......... .......... .......... .......... ........yes
checking whether make supports nested variables... yes
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE index.c -o index.o
checking for style of include used by make... GNU
checking for gcc... gcc
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
.. 799K
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1450K .......... .......... ........ 153M=0.5s
2022-02-03 22:14:07 (3.11 MB/s) - zstd-1.3.1.tar.gz saved [1513767]
tar zxf zstd-1.3.1.tar.gz
Checking for unistd.h... Yes.
cat: confdefs.h: No such file or directory
checking whether the C compiler works... checking whether the C compiler works... gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c
no
no
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36':
configure: error: C compiler cannot create executables
See `config.log' for more details
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100':
configure: error: C compiler cannot create executables
See `config.log' for more details
ln -s -f zstd-1.3.1 zstd
(cd zstd; make)
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd-1.3.1'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd-1.3.1/lib'
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: *** No targets specified and no makefile found. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100'
make[2]: *** No targets specified and no makefile found. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36'
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[2]: *** No rule to make target 'install'. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100'
make[2]: *** No rule to make target 'install'. Stop.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36'
make[1]: [Makefile:55: sqlite] Error 2 (ignored)
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make[1]: [Makefile:16: pcre] Error 2 (ignored)
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third eigen
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/base
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
echo "obtain Eigen..."
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/base'
Checking for stdarg.h... Yes.
obtain Eigen...
wget --no-check-certificate http://bitbucket.org/eigen/eigen/get/3.3.7.tar.bz2 -O eigen-3.3.7.tar.bz2
URL transformed to HTTPS due to an HSTS policy
--2022-02-03 22:14:07-- https://bitbucket.org/eigen/eigen/get/3.3.7.tar.bz2
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Resolving bitbucket.org... make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third eigen
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
rm -rf eigen-eigen*
rm -f libbz2.a
tar jxf eigen-3.3.7.tar.bz2
ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/entropy_common.o common/entropy_common.c
bzip2: Compressed file ends unexpectedly;
perhaps it is corrupted? *Possible* reason follows.
bzip2: Inappropriate ioctl for device
Input file = (stdin), output file = (stdout)
It is possible that the compressed file(s) have become corrupted.
You can use the -tvv option to test integrity of such files.
You can use the `bzip2recover' program to attempt to recover
data from undamaged sections of corrupted files.
tar: Child returned status 2
tar: Error is not recoverable: exiting now
make[2]: *** [Makefile:24: eigen] Error 2
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make[1]: *** [/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/Makefile.lib:18: /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/eigen] Error 2
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/base'
make: *** [Makefile.lib:42: /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/base/lib-base.a] Error 2
make: *** Waiting for unfinished jobs....
ranlib libbz2.a
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2.c
104.192.141.1, 2406:da00:ff00::22c0:3470, 2406:da00:ff00::22c5:2ef4, ...
Connecting to bitbucket.org|104.192.141.1|:443... connected.
bam.c: In function bam_header_write:
bam.c:128:2: warning: strncpy output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
128 | strncpy(buf, "BAM\001", 4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
bam.c: In function bam_header_write:
bam.c:128:2: warning: strncpy output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
128 | strncpy(buf, "BAM\001", 4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
HTTP request sent, awaiting response... bzip2.c: In function testStream:
bzip2.c:557:37: warning: variable nread set but not used [-Wunused-but-set-variable]
557 | Int32 bzerr, bzerr_dummy, ret, nread, streamNo, i;
| ^~~~~
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2 bzip2.o -L. -lbz2
404 Not Found
2022-02-03 22:14:07 ERROR 404: Not Found.
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/pool.o common/pool.c
make[1]: *** [Makefile:84: eigen-3.3.7.tar.bz2] Error 8
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make: *** [Makefile.lib:18: /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/eigen] Error 2
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2recover.c
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2recover bzip2recover.o
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/error_private.o common/error_private.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
Doing 6 tests (3 compress, 3 uncompress) ...
If there's a problem, things might stop at this point.
./bzip2 -1 < sample1.ref > sample1.rb2
./bzip2 -2 < sample2.ref > sample2.rb2
./bzip2 -3 < sample3.ref > sample3.rb2
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/xxhash.o common/xxhash.c
./bzip2 -d < sample1.bz2 > sample1.tst
./bzip2 -d < sample2.bz2 > sample2.tst
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
./bzip2 -ds < sample3.bz2 > sample3.tst
cmp sample1.bz2 sample1.rb2
cmp sample2.bz2 sample2.rb2
cmp sample3.bz2 sample3.rb2
cmp sample1.tst sample1.ref
cmp sample2.tst sample2.ref
cmp sample3.tst sample3.ref
If you got this far and the 'cmp's didn't complain, it looks
like you're in business.
To install in /usr/local/bin, /usr/local/lib, /usr/local/man and
/usr/local/include, type
make install
To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type
make install PREFIX=/xxx/yyy
If you are (justifiably) paranoid and want to see what 'make install'
is going to do, you can first do
make -n install or
make -n install PREFIX=/xxx/yyy respectively.
The -n instructs make to show the commands it would execute, but
not actually execute them.
Instructions for use are in the preformatted manual page, in the file
bzip2.txt. For more detailed documentation, read the full manual.
It is available in Postscript form (manual.ps), PDF form (manual.pdf),
and HTML form (manual.html).
You can also do "bzip2 --help" to see some helpful information.
"bzip2 -L" displays the software license.
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/bzip2-1.0.6'
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/fse_decompress.o common/fse_decompress.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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
Checking for vsnprintf() in stdio.h... Yes.
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/threading.o common/threading.c
Checking for return value of vsnprintf()... Yes.
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bedidx.c -o bedidx.o
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/zstd_common.o common/zstd_common.c
bam_pileup.c: In function resolve_cigar2:
bam_pileup.c:75:9: warning: variable is_head set but not used [-Wunused-but-set-variable]
75 | int k, is_head = 0;
| ^~~~~~~
bam_pileup.c: In function resolve_cigar2:
bam_pileup.c:75:9: warning: variable is_head set but not used [-Wunused-but-set-variable]
75 | int k, is_head = 0;
| ^~~~~~~
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o compress/huf_compress.o compress/huf_compress.c
ar -csru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE main.c -o main.o
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
Checking for attribute(visibility) support... Yes.
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o compress/zstdmt_compress.o compress/zstdmt_compress.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zlib-1.2.8'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o example.o test/example.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
main.c: In function main:
main.c:161:5: warning: this if clause does not guard... [-Wmisleading-indentation]
161 | if ( conf_ptr )
| ^~
main.c:164:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the if
164 | if (skip >= 0) conf.line_skip = skip;
| ^~
main.c:181:5: warning: this if clause does not guard... [-Wmisleading-indentation]
181 | if (reheader)
| ^~
main.c:184:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the if
184 | struct stat stat_tbi,stat_vcf;
| ^~~~~~
gcc -I../zlib-1.2.8 -g -Wall -O2 -fPIC -o tabix main.o -L. -ltabix -lm -L../zlib-1.2.8 -lz
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bgzip.c -o bgzip.o
razf.c: In function razf_open_w:
razf.c:178:2: warning: strncpy output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
178 | strncpy((char*)rz->header->extra, "RAZF", 4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function razf_open_w:
razf.c:178:2: warning: strncpy output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
178 | strncpy((char*)rz->header->extra, "RAZF", 4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o adler32.o adler32.c
gcc -I../zlib-1.2.8 -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/tabix-0.2.6'
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/tabix-0.2.6'
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
In file included from compress/zstdmt_compress.c:25:
./common/threading.h:82:25: error: expected ;, identifier or ( before int
82 | #define pthread_mutex_t int /* #define rather than typedef, because sometimes pthread support is implicit, resulting in duplicated symbols */
| ^~~
./common/threading.h:82:25: warning: useless type name in empty declaration
In file included from compress/zstdmt_compress.c:25:
./common/threading.h:88:24: error: expected ;, identifier or ( before int
88 | #define pthread_cond_t int
| ^~~
./common/threading.h:88:24: warning: useless type name in empty declaration
make[3]: *** [<builtin>: compress/zstdmt_compress.o] Error 1
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd-1.3.1/lib'
make[2]: *** [Makefile:56: lib-release] Error 2
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd-1.3.1'
make[1]: *** [Makefile:60: zstd] Error 2
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make: *** [Makefile.lib:36: /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd/lib/libzstd.a] Error 2
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o crc32.o crc32.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o deflate.o deflate.c
faidx.c: In function fai_load:
faidx.c:277:5: warning: this else clause does not guard... [-Wmisleading-indentation]
277 | else
| ^~~~
faidx.c:280:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the else
280 | if (fp == 0) {
| ^~
faidx.c: In function fai_load:
faidx.c:277:5: warning: this else clause does not guard... [-Wmisleading-indentation]
277 | else
| ^~~~
faidx.c:280:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the else
280 | if (fp == 0) {
| ^~
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o infback.o infback.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inffast.o inffast.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inflate.o inflate.c
bam_reheader.c: In function bam_reheader:
bam_reheader.c:12:16: warning: variable old set but not used [-Wunused-but-set-variable]
12 | bam_header_t *old;
| ^~~
bam_reheader.c: In function bam_reheader:
bam_reheader.c:12:16: warning: variable old set but not used [-Wunused-but-set-variable]
12 | bam_header_t *old;
| ^~~
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o trees.o trees.c
kprobaln.c: In function kpa_glocal:
kprobaln.c:78:21: warning: variable is_diff set but not used [-Wunused-but-set-variable]
78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
| ^~~~~~~
kprobaln.c: In function kpa_glocal:
kprobaln.c:78:21: warning: variable is_diff set but not used [-Wunused-but-set-variable]
78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
| ^~~~~~~
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o zutil.o zutil.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o compress.o compress.c
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
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[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19'
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/bcftools'
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19'
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/bcftools'
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
bcf.c: In function bcf_fmt_core:
bcf.c:233:9: warning: variable iPL set but not used [-Wunused-but-set-variable]
233 | int iPL = -1;
| ^~~
bcf.c: In function bcf_fmt_core:
bcf.c:233:9: warning: variable iPL set but not used [-Wunused-but-set-variable]
233 | int iPL = -1;
| ^~~
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
bcfutils.c: In function bcf_fit_alt:
bcfutils.c:119:9: warning: variable ipl set but not used [-Wunused-but-set-variable]
119 | int ipl=-1, igt=-1;
| ^~~
bcfutils.c: In function bcf_fix_gt:
bcfutils.c:254:5: warning: this else clause does not guard... [-Wmisleading-indentation]
254 | else
| ^~~~
bcfutils.c:256:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the else
256 | b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
| ^
bcfutils.c: In function bcf_fit_alt:
bcfutils.c:119:9: warning: variable ipl set but not used [-Wunused-but-set-variable]
119 | int ipl=-1, igt=-1;
| ^~~
bcfutils.c: In function bcf_fix_gt:
bcfutils.c:254:5: warning: this else clause does not guard... [-Wmisleading-indentation]
254 | else
| ^~~~
bcfutils.c:256:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the else
256 | b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
| ^
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
em.c: In function bcf_em1:
em.c:174:12: warning: variable n2 set but not used [-Wunused-but-set-variable]
174 | int i, n, n2;
| ^~
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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
ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example example.o -L. libz.a
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o minigzip.o test/minigzip.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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 -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -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
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/bcftools'
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/misc'
make[3]: Nothing to be done for 'lib'.
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/misc'
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 '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19'
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/bcftools'
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/misc'
make[3]: Nothing to be done for 'lib'.
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/misc'
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19'
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c
gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o libz.so.1.2.8 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo -lc -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib
rm -f libz.so libz.so.1
ln -s libz.so.1.2.8 libz.so
ln -s libz.so.1.2.8 libz.so.1
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o examplesh example.o -L. libz.so.1.2.8
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzipsh minigzip.o -L. libz.so.1.2.8
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o example64.o test/example.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example64 example64.o -L. libz.a
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o test/minigzip.c
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L. libz.a
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zlib-1.2.8'
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third'
(at easybuild/site-packages/easybuild-framework/easybuild/tools/run.py:618 in parse_cmd_output)
== 2022-02-03 22:14:17,739 build_log.py:266 INFO ... (took 11 secs)
== 2022-02-03 22:14:17,742 filetools.py:1971 INFO Removing lock /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock...
== 2022-02-03 22:14:17,743 filetools.py:380 INFO Path /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock successfully removed.
== 2022-02-03 22:14:17,744 filetools.py:1975 INFO Lock removed: /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock
== 2022-02-03 22:14:17,744 easyblock.py:3986 WARNING build failed (first 300 chars): cmd " make -j 8 " exited with exit code 2 and output:
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third cnpy
make -C /tmp/mboisson/av
== 2022-02-03 22:14:17,744 easyblock.py:310 INFO Closing log for application name rvtests version 2.1.0
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