(partial) EasyBuild log for failed build of /scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/Centrifuge-1.0.3-foss-2018b.eb (PR #8714)

Centrifuge-1.0.3-foss-2018b_partial.log

== 2019-08-09 17:04:04,784 easyblock.py:279 INFO This is EasyBuild 3.9.3 (framework: 3.9.3, easyblocks: 3.9.3) on host worker01.cluster.bc2.ch.
== 2019-08-09 17:04:04,784 easyblock.py:285 INFO This is easyblock ConfigureMake from module easybuild.easyblocks.generic.configuremake (/scicore/soft/apps/EasyBuild/3.9.3/lib/python2.7/site-packages/easybuild_easyblocks-3.9.3-py2.7.egg/easybuild/easyblocks/generic/configuremake.pyo)
== 2019-08-09 17:04:04,784 easyblock.py:840 INFO Build dir set to /scratch/escobar/easybuild/Centrifuge/1.0.3/foss-2018b
== 2019-08-09 17:04:04,784 easyblock.py:900 INFO Software install dir set to /scicore/home/scicore/escobar/.local/easybuild/software/Centrifuge/1.0.3-foss-2018b
== 2019-08-09 17:04:04,785 easyblock.py:905 INFO Module install dir set to /scicore/home/scicore/escobar/.local/easybuild/modules/all
== 2019-08-09 17:04:04,785 easyblock.py:264 INFO Init completed for application name Centrifuge version 1.0.3
== 2019-08-09 17:04:04,785 easyblock.py:3020 INFO Obtained application instance of for Centrifuge (easyblock: ConfigureMake)
== 2019-08-09 17:04:04,785 one.py:146 INFO Skipping reformatting value for parameter 'toolchain'
== 2019-08-09 17:04:04,787 filetools.py:1217 INFO Creating directory /scratch/escobar/easybuild/tmp/eb-i9_KH1/reprod_20190809170404_34827 (parents: True, set_gid: False, sticky: False)
== 2019-08-09 17:04:04,787 easyblock.py:3190 INFO Dumped easyconfig instance to /scratch/escobar/easybuild/tmp/eb-i9_KH1/reprod_20190809170404_34827/Centrifuge-1.0.3-foss-2018b.eb
== 2019-08-09 17:04:04,787 filetools.py:1217 INFO Creating directory /scratch/escobar/easybuild/tmp/eb-i9_KH1/reprod_20190809170404_34827/easyblocks (parents: True, set_gid: False, sticky: False)
== 2019-08-09 17:04:04,788 filetools.py:1687 INFO /scicore/soft/apps/EasyBuild/3.9.3/lib/python2.7/site-packages/easybuild_easyblocks-3.9.3-py2.7.egg/easybuild/easyblocks/generic/configuremake.py copied to /scratch/escobar/easybuild/tmp/eb-i9_KH1/reprod_20190809170404_34827/easyblocks/configuremake.py
== 2019-08-09 17:04:04,788 easyblock.py:3205 INFO Dumped easyblock configuremake.py required for reproduction to /scratch/escobar/easybuild/tmp/eb-i9_KH1/reprod_20190809170404_34827/easyblocks
== 2019-08-09 17:04:04,789 easyconfig.py:1599 WARNING Unable to resolve template value  prefix=%(installdir)s with dict {'bitbucket_account': 'centrifuge', 'nameletterlower': 'c', 'versionsuffix': '', 'toolchain_name': 'foss', 'namelower': 'centrifuge', 'version_minor': '0', 'arch': 'x86_64', 'name': 'Centrifuge', 'versionprefix': '', 'version_major': '1', 'nameletter': 'C', 'version_major_minor': '1.0', 'version': '1.0.3', 'github_account': 'centrifuge', 'toolchain_version': '2018b'}
== 2019-08-09 17:04:04,789 easyblock.py:1601 INFO Number of iterations to perform for central part of installation procedure: 1
== 2019-08-09 17:04:04,789 build_log.py:252 INFO building and installing Centrifuge/1.0.3-foss-2018b...
== 2019-08-09 17:04:04,789 build_log.py:252 INFO fetching files...
== 2019-08-09 17:04:04,789 easyblock.py:2800 INFO Starting fetch step
== 2019-08-09 17:04:04,790 easyblock.py:2806 INFO Running method fetch_step part of step fetch
== 2019-08-09 17:04:04,790 easyblock.py:1682 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2019-08-09 17:04:04,790 filetools.py:396 INFO Command eb found at /scicore/soft/apps/EasyBuild/3.9.3/bin/eb
== 2019-08-09 17:04:04,791 easyblock.py:668 INFO Found file v1.0.3.tar.gz at /scicore/home/scicore/escobar/.local/easybuild/sources/c/Centrifuge/v1.0.3.tar.gz
== 2019-08-09 17:04:04,791 easyblock.py:393 INFO Added sources: [{'path': '/scicore/home/scicore/escobar/.local/easybuild/sources/c/Centrifuge/v1.0.3.tar.gz', 'cmd': None, 'finalpath': '/scratch/escobar/easybuild/Centrifuge/1.0.3/foss-2018b', 'name': 'v1.0.3.tar.gz', 'checksum': '71340f5c0c20dd4f7c4d98ea87f9edcbb1443fff8434e816a5465cbebaca9343'}]
== 2019-08-09 17:04:04,791 filetools.py:396 INFO Command eb found at /scicore/soft/apps/EasyBuild/3.9.3/bin/eb
== 2019-08-09 17:04:04,792 easyblock.py:668 INFO Found file centrifuge_1.0.3_compile_error_gcc72.patch at /scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/centrifuge_1.0.3_compile_error_gcc72.patch
== 2019-08-09 17:04:04,792 easyblock.py:459 INFO Added patches: [{'path': '/scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/centrifuge_1.0.3_compile_error_gcc72.patch', 'name': 'centrifuge_1.0.3_compile_error_gcc72.patch', 'checksum': 'af83fb8e1c730b1afb56425e80cb50222867f9af71ee14df28c62f38ea0fc9c3'}]
== 2019-08-09 17:04:04,795 easyblock.py:1733 INFO md5 checksum for /scicore/home/scicore/escobar/.local/easybuild/sources/c/Centrifuge/v1.0.3.tar.gz: 4ab20730ae43f26a98b754d83213e10c
== 2019-08-09 17:04:04,799 easyblock.py:1733 INFO sha256 checksum for /scicore/home/scicore/escobar/.local/easybuild/sources/c/Centrifuge/v1.0.3.tar.gz: 71340f5c0c20dd4f7c4d98ea87f9edcbb1443fff8434e816a5465cbebaca9343
== 2019-08-09 17:04:04,799 easyblock.py:1733 INFO md5 checksum for /scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/centrifuge_1.0.3_compile_error_gcc72.patch: e1a68b0fd7fdf09b6c4387811112a9a8
== 2019-08-09 17:04:04,799 easyblock.py:1733 INFO sha256 checksum for /scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/centrifuge_1.0.3_compile_error_gcc72.patch: af83fb8e1c730b1afb56425e80cb50222867f9af71ee14df28c62f38ea0fc9c3
== 2019-08-09 17:04:04,799 easyblock.py:1768 INFO Checking dirs that need to be created: ['/scicore/home/scicore/escobar/.local/easybuild/software/Centrifuge/1.0.3-foss-2018b', '/scicore/home/scicore/escobar/.local/easybuild/modules/all/Centrifuge', '/scicore/home/scicore/escobar/.local/easybuild/modules/bio/Centrifuge']
== 2019-08-09 17:04:04,800 configuremake.py:123 INFO Found recent config.guess at /scicore/home/scicore/escobar/.local/easybuild/sources/generic/eb_v3.9.3/ConfigureMake/config.guess, using it if required
== 2019-08-09 17:04:04,800 build_log.py:252 INFO creating build dir, resetting environment...
== 2019-08-09 17:04:04,800 easyblock.py:2800 INFO Starting ready step
== 2019-08-09 17:04:04,800 easyblock.py:2806 INFO Running method check_readiness_step part of step ready
== 2019-08-09 17:04:04,801 run.py:192 INFO running cmd: ulimit -u 
== 2019-08-09 17:04:04,809 easyblock.py:1620 INFO Setting parallelism: 20
== 2019-08-09 17:04:04,906 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to  (previous value: '')
== 2019-08-09 17:04:04,907 environment.py:97 INFO Environment variable LD_PRELOAD set to  (previous value: '')
== 2019-08-09 17:04:04,907 easyblock.py:1634 WARNING Loaded modules detected: ['EasyBuild/3.9.3']
== 2019-08-09 17:04:04,908 easyblock.py:2806 INFO Running method make_builddir part of step ready
== 2019-08-09 17:04:04,908 easyblock.py:925 INFO Found old directory /scratch/escobar/easybuild/Centrifuge/1.0.3/foss-2018b
== 2019-08-09 17:04:04,908 filetools.py:1313 INFO Path /scratch/escobar/easybuild/Centrifuge/1.0.3/foss-2018b successfully removed.
== 2019-08-09 17:04:04,908 easyblock.py:932 INFO Removed old directory /scratch/escobar/easybuild/Centrifuge/1.0.3/foss-2018b
== 2019-08-09 17:04:04,909 filetools.py:1217 INFO Creating directory /scratch/escobar/easybuild/Centrifuge/1.0.3/foss-2018b (parents: True, set_gid: False, sticky: False)
== 2019-08-09 17:04:04,909 easyblock.py:2806 INFO Running method reset_env part of step ready
== 2019-08-09 17:04:04,910 easyblock.py:2806 INFO Running method handle_iterate_opts part of step ready
== 2019-08-09 17:04:04,910 build_log.py:252 INFO unpacking...
== 2019-08-09 17:04:04,911 easyblock.py:2800 INFO Starting source step
== 2019-08-09 17:04:04,911 easyblock.py:2806 INFO Running method checksum_step part of step source
== 2019-08-09 17:04:04,918 easyblock.py:1784 INFO Checksum verification for /scicore/home/scicore/escobar/.local/easybuild/sources/c/Centrifuge/v1.0.3.tar.gz using 71340f5c0c20dd4f7c4d98ea87f9edcbb1443fff8434e816a5465cbebaca9343 passed.
== 2019-08-09 17:04:04,918 easyblock.py:1784 INFO Checksum verification for /scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/centrifuge_1.0.3_compile_error_gcc72.patch using af83fb8e1c730b1afb56425e80cb50222867f9af71ee14df28c62f38ea0fc9c3 passed.
== 2019-08-09 17:04:04,918 easyblock.py:2806 INFO Running method extract_step part of step source
== 2019-08-09 17:04:04,918 easyblock.py:1852 INFO Unpacking source v1.0.3.tar.gz
== 2019-08-09 17:04:04,920 run.py:192 INFO running cmd: tar xzf /scicore/home/scicore/escobar/.local/easybuild/sources/c/Centrifuge/v1.0.3.tar.gz 
== 2019-08-09 17:04:05,022 build_log.py:252 INFO patching...
== 2019-08-09 17:04:05,023 easyblock.py:2800 INFO Starting patch step
== 2019-08-09 17:04:05,023 easyblock.py:2806 INFO Running method patch_step part of step patch
== 2019-08-09 17:04:05,024 easyblock.py:1864 INFO Applying patch centrifuge_1.0.3_compile_error_gcc72.patch
== 2019-08-09 17:04:05,026 run.py:192 INFO running cmd: patch -b -p1 -i /scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/centrifuge_1.0.3_compile_error_gcc72.patch 
== 2019-08-09 17:04:05,035 run.py:559 INFO parse_log_for_error msg: Command used: patch -b -p1 -i /scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/centrifuge_1.0.3_compile_error_gcc72.patch
== 2019-08-09 17:04:05,036 run.py:561 INFO parse_log_for_error (some may be harmless) regExp (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w) found:
Hunk #1 FAILED at 41.
Hunk #4 FAILED at 428.
2 out of 7 hunks FAILED -- saving rejects to file classifier.h.rej
== 2019-08-09 17:04:05,036 run.py:518 WARNING Found 3 errors in command output (output: Hunk #1 FAILED at 41., Hunk #4 FAILED at 428., 2 out of 7 hunks FAILED -- saving rejects to file classifier.h.rej)
== 2019-08-09 17:04:05,041 build_log.py:163 ERROR EasyBuild crashed with an error (at ?:124 in __init__): Couldn't apply patch file /scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/centrifuge_1.0.3_compile_error_gcc72.patch. Process exited with code 1: patching file classifier.h
Hunk #1 FAILED at 41.
Hunk #3 succeeded at 77 with fuzz 2.
Hunk #4 FAILED at 428.
Hunk #7 succeeded at 1026 (offset -10 lines).
2 out of 7 hunks FAILED -- saving rejects to file classifier.h.rej
 (at easybuild/tools/filetools.py:1019 in apply_patch)
== 2019-08-09 17:04:05,041 easyblock.py:3050 WARNING build failed (first 300 chars): Couldn't apply patch file /scratch/escobar/easybuild/tmp/eb-i9_KH1/files_pr8714/c/Centrifuge/centrifuge_1.0.3_compile_error_gcc72.patch. Process exited with code 1: patching file classifier.h
Hunk #1 FAILED at 41.
Hunk #3 succeeded at 77 with fuzz 2.
Hunk #4 FAILED at 428.
Hunk #7 succeeded at 1026 
== 2019-08-09 17:04:05,042 easyblock.py:294 INFO Closing log for application name Centrifuge version 1.0.3