Created
June 30, 2020 18:02
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(partial) EasyBuild log for failed build of /tmp/pescobar/eb-tmp/eb-scmmw172/files_pr10888/s/seqtk/seqtk-1.3-GCC-9.3.0.eb (PR #10888)
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| == 2020-06-30 20:02:00,265 easyblock.py:280 INFO This is EasyBuild 4.2.1 (framework: 4.2.1, easyblocks: 4.2.1) on host generoso-c1-s-1. | |
| == 2020-06-30 20:02:00,265 easyblock.py:286 INFO This is easyblock ConfigureMake from module easybuild.easyblocks.generic.configuremake (/users/pescobar/.virtualenvs/eb-4.2.1/lib/python3.6/site-packages/easybuild/easyblocks/generic/configuremake.py) | |
| == 2020-06-30 20:02:00,265 easyblock.py:843 INFO Build dir set to /tmp/pescobar/eb-build/seqtk/1.3/GCC-9.3.0 | |
| == 2020-06-30 20:02:00,265 easyblock.py:903 INFO Software install dir set to /users/pescobar/.local/easybuild/software/seqtk/1.3-GCC-9.3.0 | |
| == 2020-06-30 20:02:00,265 easyblock.py:908 INFO Module install dir set to /users/pescobar/.local/easybuild/modules/all | |
| == 2020-06-30 20:02:00,266 easyblock.py:265 INFO Init completed for application name seqtk version 1.3 | |
| == 2020-06-30 20:02:00,266 easyblock.py:3208 INFO Obtained application instance of for seqtk (easyblock: ConfigureMake) | |
| == 2020-06-30 20:02:00,266 one.py:159 INFO Skipping reformatting value for parameter 'toolchain' | |
| == 2020-06-30 20:02:00,267 filetools.py:1495 INFO Creating directory /tmp/pescobar/eb-tmp/eb-scmmw172/reprod_20200630200200_92554 (parents: True, set_gid: False, sticky: False) | |
| == 2020-06-30 20:02:00,267 easyblock.py:3385 INFO Dumped easyconfig instance to /tmp/pescobar/eb-tmp/eb-scmmw172/reprod_20200630200200_92554/seqtk-1.3-GCC-9.3.0.eb | |
| == 2020-06-30 20:02:00,268 filetools.py:1495 INFO Creating directory /tmp/pescobar/eb-tmp/eb-scmmw172/reprod_20200630200200_92554/easyblocks (parents: True, set_gid: False, sticky: False) | |
| == 2020-06-30 20:02:00,269 filetools.py:2014 INFO /users/pescobar/.virtualenvs/eb-4.2.1/lib/python3.6/site-packages/easybuild/easyblocks/generic/configuremake.py copied to /tmp/pescobar/eb-tmp/eb-scmmw172/reprod_20200630200200_92554/easyblocks/configuremake.py | |
| == 2020-06-30 20:02:00,269 easyblock.py:3400 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/pescobar/eb-tmp/eb-scmmw172/reprod_20200630200200_92554/easyblocks | |
| == 2020-06-30 20:02:00,269 easyblock.py:1635 INFO Number of iterations to perform for central part of installation procedure: 1 | |
| == 2020-06-30 20:02:00,270 build_log.py:265 INFO building and installing seqtk/1.3-GCC-9.3.0... | |
| == 2020-06-30 20:02:00,271 filetools.py:1597 INFO Lock /users/pescobar/.local/easybuild/software/.locks/_users_pescobar_.local_easybuild_software_seqtk_1.3-GCC-9.3.0.lock does not exist | |
| == 2020-06-30 20:02:00,272 filetools.py:1538 INFO Creating lock at /users/pescobar/.local/easybuild/software/.locks/_users_pescobar_.local_easybuild_software_seqtk_1.3-GCC-9.3.0.lock... | |
| == 2020-06-30 20:02:00,272 filetools.py:1495 INFO Creating directory /users/pescobar/.local/easybuild/software/.locks/_users_pescobar_.local_easybuild_software_seqtk_1.3-GCC-9.3.0.lock (parents: True, set_gid: False, sticky: False) | |
| == 2020-06-30 20:02:00,272 filetools.py:1547 INFO Lock created: /users/pescobar/.local/easybuild/software/.locks/_users_pescobar_.local_easybuild_software_seqtk_1.3-GCC-9.3.0.lock | |
| == 2020-06-30 20:02:00,272 build_log.py:265 INFO fetching files... | |
| == 2020-06-30 20:02:00,272 easyblock.py:2968 INFO Starting fetch step | |
| == 2020-06-30 20:02:00,273 easyblock.py:2974 INFO Running method fetch_step part of step fetch | |
| == 2020-06-30 20:02:00,273 easyblock.py:1744 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version | |
| == 2020-06-30 20:02:00,273 tools.py:266 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /users/pescobar/.virtualenvs/eb-4.2.1/bin/eb | |
| == 2020-06-30 20:02:00,273 tools.py:280 INFO Also considering installation prefix /users/pescobar/.virtualenvs/eb-4.2.1 (determined via path to 'eb' script)... | |
| == 2020-06-30 20:02:00,286 easyblock.py:671 INFO Found file v1.3.tar.gz at /shared/maintainers/sources/s/seqtk/v1.3.tar.gz | |
| == 2020-06-30 20:02:00,287 easyblock.py:394 INFO Added sources: [{'name': 'v1.3.tar.gz', 'path': '/shared/maintainers/sources/s/seqtk/v1.3.tar.gz', 'cmd': None, 'checksum': '5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563', 'finalpath': '/tmp/pescobar/eb-build/seqtk/1.3/GCC-9.3.0'}] | |
| == 2020-06-30 20:02:00,287 easyblock.py:1785 INFO no patches provided | |
| == 2020-06-30 20:02:00,300 easyblock.py:1795 INFO md5 checksum for /shared/maintainers/sources/s/seqtk/v1.3.tar.gz: 39a499431a10fe2412925a53ecfbab2b | |
| == 2020-06-30 20:02:00,300 easyblock.py:1795 INFO sha256 checksum for /shared/maintainers/sources/s/seqtk/v1.3.tar.gz: 5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563 | |
| == 2020-06-30 20:02:00,300 easyblock.py:1830 INFO Checking dirs that need to be created: ['/users/pescobar/.local/easybuild/software/seqtk/1.3-GCC-9.3.0', '/users/pescobar/.local/easybuild/modules/all/seqtk', '/users/pescobar/.local/easybuild/modules/bio/seqtk'] | |
| == 2020-06-30 20:02:00,301 filetools.py:1495 INFO Creating directory /users/pescobar/.local/easybuild/software/seqtk/1.3-GCC-9.3.0 (parents: True, set_gid: False, sticky: False) | |
| == 2020-06-30 20:02:00,302 filetools.py:1495 INFO Creating directory /users/pescobar/.local/easybuild/modules/all/seqtk (parents: True, set_gid: False, sticky: False) | |
| == 2020-06-30 20:02:00,303 filetools.py:1495 INFO Creating directory /users/pescobar/.local/easybuild/modules/bio/seqtk (parents: True, set_gid: False, sticky: False) | |
| == 2020-06-30 20:02:00,304 filetools.py:1495 INFO Creating directory /shared/maintainers/sources/generic/eb_v4.2.1/ConfigureMake (parents: True, set_gid: False, sticky: False) | |
| == 2020-06-30 20:02:01,161 filetools.py:614 INFO Downloaded file config.guess from url https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=59e2ce0e6b46bb47ef81b68b600ed087e14fdaad to /shared/maintainers/sources/generic/eb_v4.2.1/ConfigureMake/config.guess | |
| == 2020-06-30 20:02:01,161 filetools.py:646 INFO Successful download of file config.guess from url https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=59e2ce0e6b46bb47ef81b68b600ed087e14fdaad to path /shared/maintainers/sources/generic/eb_v4.2.1/ConfigureMake/config.guess | |
| == 2020-06-30 20:02:01,165 configuremake.py:93 INFO config.guess version: 2018-08-29 (last updated: 2020-06-30T20:02:01.159391, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c) | |
| == 2020-06-30 20:02:01,166 filetools.py:1366 INFO Adjusting permissions recursively for /shared/maintainers/sources/generic/eb_v4.2.1/ConfigureMake/config.guess | |
| == 2020-06-30 20:02:01,166 configuremake.py:162 INFO Verified config.guess at /shared/maintainers/sources/generic/eb_v4.2.1/ConfigureMake/config.guess, using it if required | |
| == 2020-06-30 20:02:01,167 build_log.py:265 INFO creating build dir, resetting environment... | |
| == 2020-06-30 20:02:01,167 easyblock.py:2968 INFO Starting ready step | |
| == 2020-06-30 20:02:01,167 easyblock.py:2974 INFO Running method check_readiness_step part of step ready | |
| == 2020-06-30 20:02:01,171 run.py:222 INFO running cmd: ulimit -u | |
| == 2020-06-30 20:02:01,176 easyblock.py:1654 INFO Setting parallelism: 1 | |
| == 2020-06-30 20:02:01,221 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to /opt/git/lib/lib:/apps/slurm/default/lib:/opt/openldap-2.4.49/lib/lib:/opt/git/lib (previous value: '/opt/git/lib/lib:/apps/slurm/default/lib:/opt/openldap-2.4.49/lib/lib:/opt/git/lib') | |
| == 2020-06-30 20:02:01,221 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '') | |
| == 2020-06-30 20:02:01,222 easyblock.py:2974 INFO Running method make_builddir part of step ready | |
| == 2020-06-30 20:02:01,223 filetools.py:1495 INFO Creating directory /tmp/pescobar/eb-build/seqtk/1.3/GCC-9.3.0 (parents: True, set_gid: False, sticky: False) | |
| == 2020-06-30 20:02:01,223 easyblock.py:2974 INFO Running method reset_env part of step ready | |
| == 2020-06-30 20:02:01,223 easyblock.py:2974 INFO Running method handle_iterate_opts part of step ready | |
| == 2020-06-30 20:02:01,224 build_log.py:265 INFO unpacking... | |
| == 2020-06-30 20:02:01,224 easyblock.py:2968 INFO Starting source step | |
| == 2020-06-30 20:02:01,224 easyblock.py:2974 INFO Running method checksum_step part of step source | |
| == 2020-06-30 20:02:01,225 easyblock.py:1846 INFO Checksum verification for /shared/maintainers/sources/s/seqtk/v1.3.tar.gz using 5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563 passed. | |
| == 2020-06-30 20:02:01,225 easyblock.py:2974 INFO Running method extract_step part of step source | |
| == 2020-06-30 20:02:01,225 easyblock.py:1933 INFO Unpacking source v1.3.tar.gz | |
| == 2020-06-30 20:02:01,225 run.py:222 INFO running cmd: tar xzf /shared/maintainers/sources/s/seqtk/v1.3.tar.gz | |
| == 2020-06-30 20:02:01,234 build_log.py:265 INFO patching... | |
| == 2020-06-30 20:02:01,234 easyblock.py:2968 INFO Starting patch step | |
| == 2020-06-30 20:02:01,235 easyblock.py:2974 INFO Running method patch_step part of step patch | |
| == 2020-06-30 20:02:01,235 build_log.py:265 INFO preparing... | |
| == 2020-06-30 20:02:01,235 easyblock.py:2968 INFO Starting prepare step | |
| == 2020-06-30 20:02:01,235 easyblock.py:2974 INFO Running method prepare_step part of step prepare | |
| == 2020-06-30 20:02:01,281 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to /opt/git/lib/lib:/apps/slurm/default/lib:/opt/openldap-2.4.49/lib/lib:/opt/git/lib (previous value: '/opt/git/lib/lib:/apps/slurm/default/lib:/opt/openldap-2.4.49/lib/lib:/opt/git/lib') | |
| == 2020-06-30 20:02:01,281 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '') | |
| == 2020-06-30 20:02:01,337 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): Missing modules for dependencies (use --robot?): zlib/1.2.11-GCCcore-9.3.0 (at easybuild/tools/toolchain/toolchain.py:502 in _check_dependencies) | |
| == 2020-06-30 20:02:01,338 filetools.py:1605 INFO Removing lock /users/pescobar/.local/easybuild/software/.locks/_users_pescobar_.local_easybuild_software_seqtk_1.3-GCC-9.3.0.lock... | |
| == 2020-06-30 20:02:01,339 filetools.py:330 INFO Path /users/pescobar/.local/easybuild/software/.locks/_users_pescobar_.local_easybuild_software_seqtk_1.3-GCC-9.3.0.lock successfully removed. | |
| == 2020-06-30 20:02:01,339 filetools.py:1609 INFO Lock removed: /users/pescobar/.local/easybuild/software/.locks/_users_pescobar_.local_easybuild_software_seqtk_1.3-GCC-9.3.0.lock | |
| == 2020-06-30 20:02:01,339 easyblock.py:3238 WARNING build failed (first 300 chars): Missing modules for dependencies (use --robot?): zlib/1.2.11-GCCcore-9.3.0 | |
| == 2020-06-30 20:02:01,340 easyblock.py:295 INFO Closing log for application name seqtk version 1.3 |
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