Created
August 11, 2019 00:58
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(partial) EasyBuild log for failed build of /tmp/eb-VYWqn0/files_pr8733/v/VEP/VEP-96.0-foss-2019a-Perl-5.28.1.eb (PR #8733)
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| == 2019-08-11 02:58:29,149 easyblock.py:279 INFO This is EasyBuild 3.9.4.dev0-re1b5a09aeb98e12fe4119fe69301da2b958af5a6 (framework: 3.9.4.dev0-re1b5a09aeb98e12fe4119fe69301da2b958af5a6, easyblocks: 3.9.4.dev0-r4a3fd740aa84f33ef6314231ad2b694549f6930e) on host login2.cerberus.os. | |
| == 2019-08-11 02:58:29,149 easyblock.py:285 INFO This is easyblock EB_VEP from module easybuild.easyblocks.vep (/u/adomingo/src/easybuild-easyblocks/easybuild/easyblocks/v/vep.pyo) | |
| == 2019-08-11 02:58:29,149 easyblock.py:840 INFO Build dir set to /u/adomingo/.local/easybuild/build/VEP/96.0/foss-2019a-Perl-5.28.1 | |
| == 2019-08-11 02:58:29,149 easyblock.py:900 INFO Software install dir set to /u/adomingo/.local/easybuild/software/VEP/96.0-foss-2019a-Perl-5.28.1 | |
| == 2019-08-11 02:58:29,149 easyblock.py:905 INFO Module install dir set to /u/adomingo/.local/easybuild/modules/all | |
| == 2019-08-11 02:58:29,149 easyblock.py:264 INFO Init completed for application name VEP version 96.0 | |
| == 2019-08-11 02:58:29,149 easyblock.py:3020 INFO Obtained application instance of for VEP (easyblock: None) | |
| == 2019-08-11 02:58:29,150 one.py:146 INFO Skipping reformatting value for parameter 'toolchain' | |
| == 2019-08-11 02:58:29,150 filetools.py:1217 INFO Creating directory /tmp/eb-VYWqn0/reprod_20190811025829_69526 (parents: True, set_gid: False, sticky: False) | |
| == 2019-08-11 02:58:29,151 easyblock.py:3190 INFO Dumped easyconfig instance to /tmp/eb-VYWqn0/reprod_20190811025829_69526/VEP-96.0-foss-2019a-Perl-5.28.1.eb | |
| == 2019-08-11 02:58:29,151 filetools.py:1217 INFO Creating directory /tmp/eb-VYWqn0/reprod_20190811025829_69526/easyblocks (parents: True, set_gid: False, sticky: False) | |
| == 2019-08-11 02:58:29,184 filetools.py:1687 INFO /u/adomingo/src/easybuild-easyblocks/easybuild/easyblocks/v/vep.py copied to /tmp/eb-VYWqn0/reprod_20190811025829_69526/easyblocks/vep.py | |
| == 2019-08-11 02:58:29,184 easyblock.py:3205 INFO Dumped easyblock vep.py required for reproduction to /tmp/eb-VYWqn0/reprod_20190811025829_69526/easyblocks | |
| == 2019-08-11 02:58:29,185 easyblock.py:1601 INFO Number of iterations to perform for central part of installation procedure: 1 | |
| == 2019-08-11 02:58:29,185 build_log.py:252 INFO building and installing VEP/96.0-foss-2019a-Perl-5.28.1... | |
| == 2019-08-11 02:58:29,185 build_log.py:252 INFO fetching files... | |
| == 2019-08-11 02:58:29,186 easyblock.py:2800 INFO Starting fetch step | |
| == 2019-08-11 02:58:29,186 easyblock.py:2806 INFO Running method fetch_step part of step fetch | |
| == 2019-08-11 02:58:29,186 easyblock.py:1682 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version | |
| == 2019-08-11 02:58:29,187 filetools.py:396 INFO Command eb found at /u/adomingo/src/easybuild-framework/eb | |
| == 2019-08-11 02:58:29,189 easyblock.py:668 INFO Found file 96.0.tar.gz at /u/adomingo/.local/easybuild/sources/v/VEP/96.0.tar.gz | |
| == 2019-08-11 02:58:29,189 easyblock.py:393 INFO Added sources: [{'path': '/u/adomingo/.local/easybuild/sources/v/VEP/96.0.tar.gz', 'cmd': None, 'finalpath': '/u/adomingo/.local/easybuild/build/VEP/96.0/foss-2019a-Perl-5.28.1', 'name': '96.0.tar.gz', 'checksum': '338f4774683da45e53bdf9a2cfffad4803df53fc4d3ee72817a9e79e63e513f7'}] | |
| == 2019-08-11 02:58:29,190 easyblock.py:1723 INFO no patches provided | |
| == 2019-08-11 02:58:29,302 easyblock.py:1733 INFO md5 checksum for /u/adomingo/.local/easybuild/sources/v/VEP/96.0.tar.gz: e48d26d66b6e5b0466893958fb7d8161 | |
| == 2019-08-11 02:58:29,433 easyblock.py:1733 INFO sha256 checksum for /u/adomingo/.local/easybuild/sources/v/VEP/96.0.tar.gz: 338f4774683da45e53bdf9a2cfffad4803df53fc4d3ee72817a9e79e63e513f7 | |
| == 2019-08-11 02:58:29,433 filetools.py:396 INFO Command eb found at /u/adomingo/src/easybuild-framework/eb | |
| == 2019-08-11 02:58:29,434 easyblock.py:668 INFO Found file 2.3.2.tar.gz at /u/adomingo/.local/easybuild/sources/v/VEP/extensions/2.3.2.tar.gz | |
| == 2019-08-11 02:58:29,435 easyblock.py:528 INFO md5 checksum for /u/adomingo/.local/easybuild/sources/v/VEP/extensions/2.3.2.tar.gz: 87c23e54ad4383470cb5e1f8ef7bdc79 | |
| == 2019-08-11 02:58:29,435 easyblock.py:528 INFO sha256 checksum for /u/adomingo/.local/easybuild/sources/v/VEP/extensions/2.3.2.tar.gz: aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5 | |
| == 2019-08-11 02:58:29,435 easyblock.py:534 INFO Checksum for extension source 2.3.2.tar.gz verified | |
| == 2019-08-11 02:58:29,435 easyblock.py:456 INFO Fetched extension patches: [] | |
| == 2019-08-11 02:58:29,436 easyblock.py:1768 INFO Checking dirs that need to be created: ['/u/adomingo/.local/easybuild/software/VEP/96.0-foss-2019a-Perl-5.28.1', '/u/adomingo/.local/easybuild/modules/all/VEP', '/u/adomingo/.local/easybuild/modules/bio/VEP'] | |
| == 2019-08-11 02:58:29,436 build_log.py:252 INFO creating build dir, resetting environment... | |
| == 2019-08-11 02:58:29,436 easyblock.py:2800 INFO Starting ready step | |
| == 2019-08-11 02:58:29,436 easyblock.py:2806 INFO Running method check_readiness_step part of step ready | |
| == 2019-08-11 02:58:29,437 run.py:192 INFO running cmd: ulimit -u | |
| == 2019-08-11 02:58:29,448 easyblock.py:1620 INFO Setting parallelism: 48 | |
| == 2019-08-11 02:58:29,520 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to (previous value: '') | |
| == 2019-08-11 02:58:29,520 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '') | |
| == 2019-08-11 02:58:29,520 easyblock.py:1634 WARNING Loaded modules detected: ['EasyBuild-develop'] | |
| == 2019-08-11 02:58:29,521 easyblock.py:2806 INFO Running method make_builddir part of step ready | |
| == 2019-08-11 02:58:29,521 easyblock.py:852 INFO Changing build dir to /u/adomingo/.local/easybuild/software/VEP/96.0-foss-2019a-Perl-5.28.1 | |
| == 2019-08-11 02:58:29,521 easyblock.py:855 INFO Overriding 'cleanupoldinstall' (to False), 'cleanupoldbuild' (to True) and 'keeppreviousinstall' because we're building in the installation directory. | |
| == 2019-08-11 02:58:29,521 easyblock.py:925 INFO Found old directory /u/adomingo/.local/easybuild/software/VEP/96.0-foss-2019a-Perl-5.28.1 | |
| == 2019-08-11 02:58:29,522 filetools.py:1313 INFO Path /u/adomingo/.local/easybuild/software/VEP/96.0-foss-2019a-Perl-5.28.1 successfully removed. | |
| == 2019-08-11 02:58:29,522 easyblock.py:932 INFO Removed old directory /u/adomingo/.local/easybuild/software/VEP/96.0-foss-2019a-Perl-5.28.1 | |
| == 2019-08-11 02:58:29,522 filetools.py:1217 INFO Creating directory /u/adomingo/.local/easybuild/software/VEP/96.0-foss-2019a-Perl-5.28.1 (parents: True, set_gid: False, sticky: False) | |
| == 2019-08-11 02:58:29,523 easyblock.py:2806 INFO Running method reset_env part of step ready | |
| == 2019-08-11 02:58:29,524 easyblock.py:2806 INFO Running method handle_iterate_opts part of step ready | |
| == 2019-08-11 02:58:29,524 build_log.py:252 INFO unpacking... | |
| == 2019-08-11 02:58:29,524 easyblock.py:2800 INFO Starting source step | |
| == 2019-08-11 02:58:29,525 easyblock.py:2806 INFO Running method checksum_step part of step source | |
| == 2019-08-11 02:58:29,664 easyblock.py:1784 INFO Checksum verification for /u/adomingo/.local/easybuild/sources/v/VEP/96.0.tar.gz using 338f4774683da45e53bdf9a2cfffad4803df53fc4d3ee72817a9e79e63e513f7 passed. | |
| == 2019-08-11 02:58:29,665 easyblock.py:2806 INFO Running method extract_step part of step source | |
| == 2019-08-11 02:58:29,665 easyblock.py:1852 INFO Unpacking source 96.0.tar.gz | |
| == 2019-08-11 02:58:29,666 run.py:192 INFO running cmd: tar xzf /u/adomingo/.local/easybuild/sources/v/VEP/96.0.tar.gz --strip-components=1 | |
| == 2019-08-11 02:58:31,469 build_log.py:252 INFO patching... | |
| == 2019-08-11 02:58:31,469 easyblock.py:2800 INFO Starting patch step | |
| == 2019-08-11 02:58:31,470 easyblock.py:2806 INFO Running method patch_step part of step patch | |
| == 2019-08-11 02:58:31,470 build_log.py:252 INFO preparing... | |
| == 2019-08-11 02:58:31,471 easyblock.py:2800 INFO Starting prepare step | |
| == 2019-08-11 02:58:31,471 easyblock.py:2806 INFO Running method prepare_step part of step prepare | |
| == 2019-08-11 02:58:33,007 build_log.py:163 ERROR EasyBuild crashed with an error (at ?:124 in __init__): Missing modules for dependencies (use --robot?): BioPerl/1.7.2-GCCcore-8.2.0-Perl-5.28.1, Bio-DB-HTS/3.01-GCC-8.2.0-2.31.1-Perl-5.28.1 (at easybuild/tools/toolchain/toolchain.py:420 in _check_dependencies) | |
| == 2019-08-11 02:58:33,007 easyblock.py:3050 WARNING build failed (first 300 chars): Missing modules for dependencies (use --robot?): BioPerl/1.7.2-GCCcore-8.2.0-Perl-5.28.1, Bio-DB-HTS/3.01-GCC-8.2.0-2.31.1-Perl-5.28.1 | |
| == 2019-08-11 02:58:33,007 easyblock.py:294 INFO Closing log for application name VEP version 96.0 |
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