zao/HapCUT2-v1.3.3-GCC-12.3.0_partial.log

## HapCUT2-v1.3.3-GCC-12.3.0_partial.log
== 2024-04-17 13:32:19,175 easyblock.py:313 INFO This is EasyBuild 4.9.2.dev0-r73e917cee9473544af22f264c0d63de753dc12cb (framework: 4.9.2.dev0-r73e917cee9473544af22f264c0d63de753dc12cb, easyblocks: 4.9.2.dev0-r3e3854a9e63a49623b83f5e556ce4d99542dfa89) on host eb-mix.zao.se.
== 2024-04-17 13:32:19,175 easyblock.py:319 INFO This is easyblock MakeCp from module easybuild.easyblocks.generic.makecp (/eb/develop/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py)
== 2024-04-17 13:32:19,176 easyblock.py:1056 INFO Build dir set to /eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0
== 2024-04-17 13:32:19,176 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/software
== 2024-04-17 13:32:19,176 easyconfig.py:2653 DEBUG Determining software installation subdir for HapCUT2 EasyConfig @ /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HapCUT2-v1.3.3-GCC-12.3.0.eb
== 2024-04-17 13:32:19,176 easyconfig.py:2656 DEBUG Using fixed naming software installation subdir: HapCUT2/v1.3.3-GCC-12.3.0
== 2024-04-17 13:32:19,176 easyblock.py:1113 INFO Software install dir set to /eb/software/HapCUT2/v1.3.3-GCC-12.3.0
== 2024-04-17 13:32:19,176 config.py:699 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /eb/modules
== 2024-04-17 13:32:19,176 easyblock.py:1118 INFO Module install dir set to /eb/modules/all
== 2024-04-17 13:32:19,176 easyblock.py:288 INFO Init completed for application name HapCUT2 version v1.3.3
== 2024-04-17 13:32:19,176 easyblock.py:4234 INFO Obtained application instance of for HapCUT2 (easyblock: MakeCp)
== 2024-04-17 13:32:19,176 easyblock.py:4247 DEBUG Skip set to False
== 2024-04-17 13:32:19,176 easyconfig.py:1702 INFO Generating template values...
== 2024-04-17 13:32:19,176 templates.py:201 DEBUG config: HapCUT2 EasyConfig @ /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HapCUT2-v1.3.3-GCC-12.3.0.eb
== 2024-04-17 13:32:19,176 templates.py:231 DEBUG version found in easyconfig is v1.3.3
== 2024-04-17 13:32:19,176 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-04-17 13:32:19,176 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-04-17 13:32:19,177 templates.py:333 DEBUG name: name, config: HapCUT2
== 2024-04-17 13:32:19,177 templates.py:333 DEBUG name: parallel, config: None
== 2024-04-17 13:32:19,177 templates.py:333 DEBUG name: version, config: v1.3.3
== 2024-04-17 13:32:19,177 templates.py:333 DEBUG name: versionsuffix, config:
== 2024-04-17 13:32:19,177 templates.py:333 DEBUG name: versionprefix, config:
== 2024-04-17 13:32:19,177 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='hapcut2', github_account='hapcut2', module_name='HapCUT2/v1.3.3', name='HapCUT2', nameletter='H', nameletterlower='h', namelower='hapcut2', sysroot='', toolchain_name='GCC', toolchain_version='12.3.0', version='v1.3.3', version_major='v1', version_major_minor='v1.3', version_minor='3', versionprefix='', versionsuffix=''
== 2024-04-17 13:32:19,177 one.py:150 DEBUG Not copying '__builtins__' variable from parsed easyconfig
== 2024-04-17 13:32:19,177 one.py:529 DEBUG Extracted comments:
{'above': {'download_instructions': ["# source_urls = ['https://github.com/vibansal/HapCUT2/archive/refs/tags/']",
                                     "# sources = ['%(version)s.tar.gz']",
                                     '']},
 'header': [],
 'inline': {},
 'iterabove': {},
 'iterinline': {},
 'tail': []}
== 2024-04-17 13:32:19,177 one.py:180 INFO Skipping reformatting value for parameter 'toolchain'
== 2024-04-17 13:32:19,178 easyconfig.py:1265 DEBUG Dumped easyconfig: easyblock = 'MakeCp'

name = 'HapCUT2'
version = 'v1.3.3'

homepage = 'https://github.com/vibansal/HapCUT2/'
description = """
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads,
designed to "just work" with excellent speed and accuracy.
We found that previously described haplotype assembly methods are specialized for specific read technologies or
protocols,
with slow or inaccurate performance on others.
With this in mind, HapCUT2 is designed for speed and accuracy across diverse sequencing technologies,
including but not limited to:

    - NGS short reads (Illumina HiSeq)
    - single-molecule long reads (PacBio and Oxford Nanopore)
    - Linked-Reads (e.g. 10X Genomics, stLFR or TELL-seq)
    - proximity-ligation (Hi-C) reads
    - high-coverage sequencing (>40x coverage-per-SNP) using above technologies
    - combinations of the above technologies (e.g. scaffold long reads with Hi-C reads)
"""

toolchain = {'name': 'GCC', 'version': '12.3.0'}

sources = [
    {'filename': '%(version)s.tar.gz', 'git_config': {'url': 'https://github.com/vibansal/', 'repo_name': '%(name)s', 'commit': '0eb7075', 'recursive': True, 'keep_git_dir': True}},
]
patches = ['HAPcut-%(version)s-Fix-Makefile.patch']
checksums = [
    {'%(version)s.tar.gz': '4ff42519d7f9ed8159d41adc94bff7c600145424f5b501b1ece7930cfdd74e9f'},
    {'HAPcut-%(version)s-Fix-Makefile.patch': '4bb81d3e317c14493cf065d09be3f24593c610c3a1bbfafbbb9833078c8d832c'},
]

dependencies = [
    ('HTSlib', '1.18'),
]

# source_urls = ['https://github.com/vibansal/HapCUT2/archive/refs/tags/']
# sources = ['%(version)s.tar.gz']

download_instructions = """
  The last version tag %(version)s does not include last modification that make it work.
  So we download source from master branch at the commit where I tested.
"""
skipsteps = ['configure']
files_to_copy = [(['build/HAPCUT2', 'build/extractHAIRS'], 'bin')]
configure_cmd = ''

sanity_check_paths = {
    'files': ['bin/HAPCUT2', 'bin/extractHAIRS'],
    'dirs': ['bin'],
}

sanity_check_commands = ['cd %(installdir)s/bin/ && HAPCUT2']

moduleclass = 'bio'

== 2024-04-17 13:32:19,178 filetools.py:1912 INFO Creating directory /eb/tmp/eb-rssr4be3/reprod_20240417133219_3215457 (parents: True, set_gid: False, sticky: False)
== 2024-04-17 13:32:19,178 easyblock.py:4488 INFO Dumped easyconfig instance to /eb/tmp/eb-rssr4be3/reprod_20240417133219_3215457/HapCUT2-v1.3.3-GCC-12.3.0.eb
== 2024-04-17 13:32:19,178 filetools.py:1912 INFO Creating directory /eb/tmp/eb-rssr4be3/reprod_20240417133219_3215457/easyblocks (parents: True, set_gid: False, sticky: False)
== 2024-04-17 13:32:19,179 filetools.py:2425 INFO /eb/develop/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py copied to /eb/tmp/eb-rssr4be3/reprod_20240417133219_3215457/easyblocks/makecp.py
== 2024-04-17 13:32:19,179 easyblock.py:4468 INFO Dumped easyblock makecp.py required for reproduction to /eb/tmp/eb-rssr4be3/reprod_20240417133219_3215457/easyblocks
== 2024-04-17 13:32:19,179 filetools.py:1931 DEBUG Not creating existing path /eb/tmp/eb-rssr4be3/reprod_20240417133219_3215457/easyblocks
== 2024-04-17 13:32:19,180 filetools.py:2425 INFO /eb/develop/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /eb/tmp/eb-rssr4be3/reprod_20240417133219_3215457/easyblocks/configuremake.py
== 2024-04-17 13:32:19,180 easyblock.py:4468 INFO Dumped easyblock configuremake.py required for reproduction to /eb/tmp/eb-rssr4be3/reprod_20240417133219_3215457/easyblocks
== 2024-04-17 13:32:19,180 easyblock.py:2239 INFO Number of iterations to perform for central part of installation procedure: 1
== 2024-04-17 13:32:19,180 build_log.py:267 INFO building and installing Compiler/GCC/12.3.0/HapCUT2/v1.3.3...
== 2024-04-17 13:32:19,182 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/software
== 2024-04-17 13:32:19,182 filetools.py:2005 INFO Lock /eb/software/.locks/_eb_software_HapCUT2_v1.3.3-GCC-12.3.0.lock does not exist
== 2024-04-17 13:32:19,182 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/software
== 2024-04-17 13:32:19,182 filetools.py:1946 INFO Creating lock at /eb/software/.locks/_eb_software_HapCUT2_v1.3.3-GCC-12.3.0.lock...
== 2024-04-17 13:32:19,182 filetools.py:1912 INFO Creating directory /eb/software/.locks/_eb_software_HapCUT2_v1.3.3-GCC-12.3.0.lock (parents: True, set_gid: False, sticky: False)
== 2024-04-17 13:32:19,183 filetools.py:1955 INFO Lock created: /eb/software/.locks/_eb_software_HapCUT2_v1.3.3-GCC-12.3.0.lock
== 2024-04-17 13:32:19,183 easyblock.py:3947 DEBUG Not skipping fetch step (skippable: False, skip: None, skipsteps: ['configure'], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False)
== 2024-04-17 13:32:19,183 build_log.py:267 INFO fetching files...
== 2024-04-17 13:32:19,184 easyblock.py:3956 INFO Starting fetch step
== 2024-04-17 13:32:19,184 easyconfig.py:1702 INFO Generating template values...
== 2024-04-17 13:32:19,184 templates.py:201 DEBUG config: HapCUT2 EasyConfig @ /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HapCUT2-v1.3.3-GCC-12.3.0.eb
== 2024-04-17 13:32:19,184 templates.py:231 DEBUG version found in easyconfig is v1.3.3
== 2024-04-17 13:32:19,184 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-04-17 13:32:19,184 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-04-17 13:32:19,184 templates.py:333 DEBUG name: name, config: HapCUT2
== 2024-04-17 13:32:19,184 templates.py:333 DEBUG name: parallel, config: None
== 2024-04-17 13:32:19,184 templates.py:333 DEBUG name: version, config: v1.3.3
== 2024-04-17 13:32:19,184 templates.py:333 DEBUG name: versionsuffix, config:
== 2024-04-17 13:32:19,184 templates.py:333 DEBUG name: versionprefix, config:
== 2024-04-17 13:32:19,184 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='hapcut2', builddir='/eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0', github_account='hapcut2', installdir='/eb/software/HapCUT2/v1.3.3-GCC-12.3.0', module_name='HapCUT2/v1.3.3', name='HapCUT2', nameletter='H', nameletterlower='h', namelower='hapcut2', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='12.3.0', version='v1.3.3', version_major='v1', version_major_minor='v1.3', version_minor='3', versionprefix='', versionsuffix=''
== 2024-04-17 13:32:19,185 easyblock.py:3964 INFO Running method fetch_step part of step fetch
== 2024-04-17 13:32:19,185 easyblock.py:2361 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2024-04-17 13:32:19,185 easyblock.py:809 INFO Considering directory in which easyconfig file is located when searching for v1.3.3.tar.gz: /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2
== 2024-04-17 13:32:19,185 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /eb/develop/easybuild-framework/eb
== 2024-04-17 13:32:19,185 tools.py:290 INFO Not considering /eb/develop (no easybuild/easyconfigs subdir found)
== 2024-04-17 13:32:19,185 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/custom/easyconfigs/easybuild/easyconfigs
== 2024-04-17 13:32:19,185 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-04-17 13:32:19,185 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/tmp/eb-rssr4be3/files_pr20380/easybuild/easyconfigs
== 2024-04-17 13:32:19,185 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/tmp/eb-rssr4be3/fake_vsc_x89ater_/easybuild/easyconfigs
== 2024-04-17 13:32:19,185 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/tmp/eb-rssr4be3/included-easyblocks-9gzi5r5h/easybuild/easyconfigs
== 2024-04-17 13:32:19,185 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/easybuild/easybuild/easyconfigs
== 2024-04-17 13:32:19,185 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-04-17 13:32:19,185 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/easybuild-easyconfigs/easybuild/easyconfigs
== 2024-04-17 13:32:19,185 tools.py:307 DEBUG Added /eb/develop/easybuild-easyconfigs/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-04-17 13:32:19,185 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/easybuild-easyblocks/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/easybuild-framework/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/vsc-install/lib/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/vsc-base/lib/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python312.zip/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.12/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.12/lib-dynload/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.12/dist-packages/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.12/dist-packages/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at ../easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/graphviz/python/easybuild/easyconfigs
== 2024-04-17 13:32:19,186 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/graphviz/python/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 easyblock.py:851 INFO Found file v1.3.3.tar.gz at /eb/sources/h/HapCUT2/v1.3.3.tar.gz
== 2024-04-17 13:32:19,187 easyblock.py:452 DEBUG File /eb/sources/h/HapCUT2/v1.3.3.tar.gz found for source v1.3.3.tar.gz
== 2024-04-17 13:32:19,187 easyblock.py:496 INFO Added sources: [{'name': 'v1.3.3.tar.gz', 'path': '/eb/sources/h/HapCUT2/v1.3.3.tar.gz', 'cmd': None, 'checksum': {'v1.3.3.tar.gz': '4ff42519d7f9ed8159d41adc94bff7c600145424f5b501b1ece7930cfdd74e9f'}, 'finalpath': '/eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0'}]
== 2024-04-17 13:32:19,187 easyblock.py:809 INFO Considering directory in which easyconfig file is located when searching for HAPcut-v1.3.3-Fix-Makefile.patch: /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2
== 2024-04-17 13:32:19,187 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /eb/develop/easybuild-framework/eb
== 2024-04-17 13:32:19,187 tools.py:290 INFO Not considering /eb/develop (no easybuild/easyconfigs subdir found)
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/custom/easyconfigs/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/tmp/eb-rssr4be3/files_pr20380/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/tmp/eb-rssr4be3/fake_vsc_x89ater_/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/tmp/eb-rssr4be3/included-easyblocks-9gzi5r5h/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/easybuild/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/easybuild-easyconfigs/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:307 DEBUG Added /eb/develop/easybuild-easyconfigs/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/easybuild-easyblocks/easybuild/easyconfigs
== 2024-04-17 13:32:19,187 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/easybuild-framework/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/vsc-install/lib/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/develop/vsc-base/lib/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python312.zip/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.12/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.12/lib-dynload/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.12/dist-packages/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.12/dist-packages/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at ../easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/graphviz/python/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/graphviz/python/easybuild/easyconfigs
== 2024-04-17 13:32:19,188 easyblock.py:851 INFO Found file HAPcut-v1.3.3-Fix-Makefile.patch at /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HAPcut-v1.3.3-Fix-Makefile.patch
== 2024-04-17 13:32:19,188 easyblock.py:520 DEBUG File /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HAPcut-v1.3.3-Fix-Makefile.patch found for patch HAPcut-v1.3.3-Fix-Makefile.patch
== 2024-04-17 13:32:19,188 easyblock.py:535 INFO Added patches: [{'name': 'HAPcut-v1.3.3-Fix-Makefile.patch', 'postinstall': False, 'path': '/eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HAPcut-v1.3.3-Fix-Makefile.patch', 'checksum': {'HAPcut-v1.3.3-Fix-Makefile.patch': '4bb81d3e317c14493cf065d09be3f24593c610c3a1bbfafbbb9833078c8d832c'}}]
== 2024-04-17 13:32:19,188 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-04-17 13:32:19,197 easyblock.py:2414 INFO md5 checksum for /eb/sources/h/HapCUT2/v1.3.3.tar.gz: 9ad7adb41b0224eb0c37ec716bfb738d
== 2024-04-17 13:32:19,197 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-04-17 13:32:19,201 easyblock.py:2414 INFO sha256 checksum for /eb/sources/h/HapCUT2/v1.3.3.tar.gz: 59b3e75f538ffb5cc586a6842049b52e92d7cfc9325bf1b9843185efe90abd89
== 2024-04-17 13:32:19,201 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-04-17 13:32:19,201 easyblock.py:2414 INFO md5 checksum for /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HAPcut-v1.3.3-Fix-Makefile.patch: f33b34ad53982b091b949623e89ada48
== 2024-04-17 13:32:19,201 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-04-17 13:32:19,201 easyblock.py:2414 INFO sha256 checksum for /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HAPcut-v1.3.3-Fix-Makefile.patch: 4bb81d3e317c14493cf065d09be3f24593c610c3a1bbfafbbb9833078c8d832c
== 2024-04-17 13:32:19,207 easyconfig.py:2640 DEBUG Determining full module name for HapCUT2 EasyConfig @ /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HapCUT2-v1.3.3-GCC-12.3.0.eb (force_visible: False)
== 2024-04-17 13:32:19,207 easyconfig.py:2617 DEBUG No alternative software name specified to determine module name with
== 2024-04-17 13:32:19,207 toolchain.py:592 DEBUG Toolchain definition for {'name': 'GCC', 'version': '12.3.0', 'toolchain': {'name': 'system', 'version': ''}, 'versionsuffix': '', 'parsed': True, 'hidden': False, 'full_mod_name': 'Core/GCC/12.3.0', 'short_mod_name': 'GCC/12.3.0', 'system': True}: {'COMPILER': ['GCC']}
== 2024-04-17 13:32:19,207 toolchain.py:61 DEBUG Obtained details for 'GCC' in toolchain '{'name': 'GCC', 'version': '12.3.0', 'toolchain': {'name': 'system', 'version': ''}, 'versionsuffix': '', 'parsed': True, 'hidden': False, 'full_mod_name': 'Core/GCC/12.3.0', 'short_mod_name': 'GCC/12.3.0', 'system': True}' from cache
== 2024-04-17 13:32:19,207 toolchain.py:136 DEBUG Found compilers [{'description': 'The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,\n as well as libraries for these languages (libstdc++, libgcj,...).', 'homepage': 'https://gcc.gnu.org/', 'name': 'GCC', 'toolchain': {'name': 'system', 'version': 'system'}, 'version': '12.3.0', 'software_license': None, 'software_license_urls': None, 'docurls': None, 'onlytcmod': False, 'toolchainopts': None, 'banned_linked_shared_libs': [], 'bitbucket_account': 'gcc', 'buildopts': '', 'checksums': [], 'configopts': '', 'cuda_compute_capabilities': [], 'download_instructions': '', 'easyblock': 'Bundle', 'easybuild_version': None, 'enhance_sanity_check': False, 'fix_bash_shebang_for': None, 'fix_perl_shebang_for': None, 'fix_python_shebang_for': None, 'github_account': 'gcc', 'hidden': False, 'installopts': '', 'maxparallel': None, 'parallel': None, 'patches': [], 'prebuildopts': '', 'preconfigopts': '', 'preinstallopts': '', 'pretestopts': '', 'postinstallcmds': [], 'postinstallpatches': [], 'postinstallmsgs': [], 'required_linked_shared_libs': [], 'runtest': None, 'bin_lib_subdirs': [], 'sanity_check_commands': [], 'sanity_check_paths': {}, 'skip': False, 'skipsteps': [], 'source_urls': [], 'sources': [], 'stop': None, 'testopts': '', 'tests': [], 'unpack_options': '', 'unwanted_env_vars': [], 'versionprefix': '', 'versionsuffix': '', 'buildininstalldir': False, 'cleanupoldbuild': True, 'cleanupoldinstall': True, 'dontcreateinstalldir': False, 'keeppreviousinstall': False, 'keepsymlinks': False, 'start_dir': None, 'allow_system_deps': [], 'builddependencies': [], 'dependencies': [{'full_mod_name': 'Core/GCCcore/12.3.0', 'short_mod_name': 'GCCcore/12.3.0', 'name': 'GCCcore', 'version': '12.3.0', 'versionsuffix': '', 'toolchain': {'name': 'system', 'version': 'system'}, 'toolchain_inherited': True, 'system': True, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'Compiler/GCCcore/12.3.0/binutils/2.40', 'short_mod_name': 'binutils/2.40', 'name': 'binutils', 'version': '2.40', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}], 'hiddendependencies': [], 'multi_deps': {}, 'multi_deps_load_default': True, 'osdependencies': [], 'moddependpaths': None, 'accept_eula': False, 'group': None, 'key': None, 'license_file': None, 'license_server': None, 'license_server_port': None, 'exts_download_dep_fail': False, 'exts_classmap': {}, 'exts_defaultclass': None, 'exts_default_options': {}, 'exts_filter': None, 'exts_list': [], 'allow_append_abs_path': False, 'allow_prepend_abs_path': False, 'include_modpath_extensions': True, 'modaliases': {}, 'modextrapaths': {}, 'modextrapaths_append': {}, 'modextravars': {}, 'modloadmsg': {}, 'modunloadmsg': {}, 'modluafooter': '', 'modaltsoftname': None, 'modtclfooter': '', 'moduleclass': 'compiler', 'moduleforceunload': False, 'moduleloadnoconflict': False, 'module_depends_on': False, 'recursive_module_unload': None, 'citing': None, 'docpaths': None, 'examples': None, 'site_contacts': None, 'upstream_contacts': None, 'usage': None, 'whatis': None, 'block': None, 'buildstats': None, 'deprecated': False, 'build_info_msg': None, 'altroot': 'GCCcore', 'altversion': 'GCCcore', 'default_component_specs': {}, 'components': (), 'sanity_check_components': [], 'sanity_check_all_components': False, 'default_easyblock': None, 'parsed': True}] for toolchain GCC ({'name': 'GCC', 'version': '12.3.0', 'toolchain': {'name': 'system', 'version': ''}, 'versionsuffix': '', 'parsed': True, 'hidden': False, 'full_mod_name': 'Core/GCC/12.3.0', 'short_mod_name': 'GCC/12.3.0', 'system': True})
== 2024-04-17 13:32:19,207 toolchain.py:592 DEBUG Toolchain definition for {'name': 'GCC', 'version': '12.3.0', 'toolchain': {'name': 'system', 'version': ''}, 'versionsuffix': '', 'parsed': True, 'hidden': False, 'full_mod_name': 'Core/GCC/12.3.0', 'short_mod_name': 'GCC/12.3.0', 'system': True}: {'COMPILER': ['GCC']}
== 2024-04-17 13:32:19,207 utilities.py:115 DEBUG Module name Compiler/GCC/12.3.0/HapCUT2/v1.3.3 validated
== 2024-04-17 13:32:19,207 easyconfig.py:2648 DEBUG Obtained valid full module name Compiler/GCC/12.3.0/HapCUT2/v1.3.3
== 2024-04-17 13:32:19,207 easyblock.py:2449 INFO Checking dirs that need to be created: ['/eb/software/HapCUT2/v1.3.3-GCC-12.3.0', '/eb/modules/all/Compiler/GCC/12.3.0/HapCUT2']
== 2024-04-17 13:32:19,207 filetools.py:1931 DEBUG Not creating existing path /eb/software/HapCUT2/v1.3.3-GCC-12.3.0
== 2024-04-17 13:32:19,207 filetools.py:1931 DEBUG Not creating existing path /eb/modules/all/Compiler/GCC/12.3.0/HapCUT2
== 2024-04-17 13:32:19,208 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-04-17 13:32:19,208 configuremake.py:95 INFO config.guess version: 2018-08-29 (last updated: 2024-04-09T17:28:48.247079, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c)
== 2024-04-17 13:32:19,208 configuremake.py:151 INFO Found config.guess at /eb/sources/generic/eb_v4.9.2.dev0/ConfigureMake/config.guess
== 2024-04-17 13:32:19,208 build_log.py:267 INFO ... (took < 1 sec)
== 2024-04-17 13:32:19,210 easyblock.py:3947 DEBUG Not skipping ready step (skippable: False, skip: None, skipsteps: ['configure'], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False)
== 2024-04-17 13:32:19,210 build_log.py:267 INFO creating build dir, resetting environment...
== 2024-04-17 13:32:19,211 easyblock.py:3956 INFO Starting ready step
== 2024-04-17 13:32:19,211 easyconfig.py:1702 INFO Generating template values...
== 2024-04-17 13:32:19,211 templates.py:201 DEBUG config: HapCUT2 EasyConfig @ /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HapCUT2-v1.3.3-GCC-12.3.0.eb
== 2024-04-17 13:32:19,211 templates.py:231 DEBUG version found in easyconfig is v1.3.3
== 2024-04-17 13:32:19,211 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-04-17 13:32:19,211 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-04-17 13:32:19,211 templates.py:333 DEBUG name: name, config: HapCUT2
== 2024-04-17 13:32:19,211 templates.py:333 DEBUG name: parallel, config: None
== 2024-04-17 13:32:19,211 templates.py:333 DEBUG name: version, config: v1.3.3
== 2024-04-17 13:32:19,211 templates.py:333 DEBUG name: versionsuffix, config:
== 2024-04-17 13:32:19,211 templates.py:333 DEBUG name: versionprefix, config:
== 2024-04-17 13:32:19,211 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='hapcut2', builddir='/eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0', github_account='hapcut2', installdir='/eb/software/HapCUT2/v1.3.3-GCC-12.3.0', module_name='HapCUT2/v1.3.3', name='HapCUT2', nameletter='H', nameletterlower='h', namelower='hapcut2', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='12.3.0', version='v1.3.3', version_major='v1', version_major_minor='v1.3', version_minor='3', versionprefix='', versionsuffix=''
== 2024-04-17 13:32:19,211 easyblock.py:3964 INFO Running method check_readiness_step part of step ready
== 2024-04-17 13:32:19,211 easyblock.py:2249 DEBUG Desired parallelism specified via 'parallel' build option: None
== 2024-04-17 13:32:19,215 systemtools.py:247 DEBUG sched_getaffinity for pid 3215457 successful
== 2024-04-17 13:32:19,215 run.py:221 DEBUG run_cmd: running cmd ulimit -u (in /home/easybuild)
== 2024-04-17 13:32:19,215 run.py:247 INFO running cmd: ulimit -u
== 2024-04-17 13:32:19,219 run.py:689 DEBUG cmd "ulimit -u" exited with exit code 0 and output:
95903

== 2024-04-17 13:32:19,219 run.py:725 DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w)
== 2024-04-17 13:32:19,219 easyblock.py:2258 INFO Setting parallelism: 12
== 2024-04-17 13:32:19,219 modules.py:812 DEBUG Current MODULEPATH: /eb/modules/all:/eb/modules/all/Core:/eb/develop/modules:/opt/modulefiles/Linux:/opt/modulefiles/Core:/opt/lmod/lmod/modulefiles/Core
== 2024-04-17 13:32:19,219 modules.py:826 DEBUG Running module command '/opt/lmod/lmod/libexec/lmod python --terse list' from /home/easybuild
== 2024-04-17 13:32:19,285 modules.py:833 DEBUG Output of module command '/opt/lmod/lmod/libexec/lmod python --terse list': stdout: import os
os.environ["MODULEPATH"] = "/eb/modules/all:/eb/modules/all/Core:/eb/develop/modules:/opt/modulefiles/Linux:/opt/modulefiles/Core:/opt/lmod/lmod/modulefiles/Core";
os.environ["_ModuleTable001_"] = "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";
os.environ["_ModuleTable002_"] = "LCAiL2ViL2RldmVsb3AvbW9kdWxlcyIsICIvb3B0L21vZHVsZWZpbGVzL0xpbnV4IiwgIi9vcHQvbW9kdWxlZmlsZXMvQ29yZSIsICIvb3B0L2xtb2QvbG1vZC9tb2R1bGVmaWxlcy9Db3JlIiwKfSwKc3lzdGVtQmFzZU1QQVRIID0gIi9vcHQvbW9kdWxlZmlsZXMvTGludXg6L29wdC9tb2R1bGVmaWxlcy9Db3JlOi9vcHQvbG1vZC9sbW9kL21vZHVsZWZpbGVzL0NvcmUiLAp9Cg==";
os.environ["_ModuleTable_Sz_"] = "2";
_mlstatus = True
; stderr: EasyBuild-develop

== 2024-04-17 13:32:19,285 modules.py:1469 DEBUG Output found in stdout, seems like '/opt/lmod/lmod/libexec/lmod python --terse list' ran fine
== 2024-04-17 13:32:19,285 easyblock.py:2310 WARNING Loaded modules detected: ['EasyBuild-develop']
== 2024-04-17 13:32:19,285 easyblock.py:3964 INFO Running method make_builddir part of step ready
== 2024-04-17 13:32:19,285 easyblock.py:1066 DEBUG Creating the build directory /eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0 (cleanup: True)
== 2024-04-17 13:32:19,285 easyblock.py:1138 INFO Found old directory /eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0
== 2024-04-17 13:32:19,285 filetools.py:383 INFO Path /eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0 successfully removed.
== 2024-04-17 13:32:19,285 easyblock.py:1146 INFO Removed old directory /eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0
== 2024-04-17 13:32:19,285 filetools.py:1912 INFO Creating directory /eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0 (parents: True, set_gid: False, sticky: False)
== 2024-04-17 13:32:19,287 easyblock.py:3964 INFO Running method reset_env part of step ready
== 2024-04-17 13:32:19,287 easyblock.py:3964 INFO Running method handle_iterate_opts part of step ready
== 2024-04-17 13:32:19,287 easyconfig.py:1702 INFO Generating template values...
== 2024-04-17 13:32:19,287 templates.py:201 DEBUG config: HapCUT2 EasyConfig @ /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HapCUT2-v1.3.3-GCC-12.3.0.eb
== 2024-04-17 13:32:19,287 templates.py:231 DEBUG version found in easyconfig is v1.3.3
== 2024-04-17 13:32:19,287 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-04-17 13:32:19,287 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-04-17 13:32:19,287 templates.py:333 DEBUG name: name, config: HapCUT2
== 2024-04-17 13:32:19,287 templates.py:333 DEBUG name: parallel, config: 12
== 2024-04-17 13:32:19,287 templates.py:333 DEBUG name: version, config: v1.3.3
== 2024-04-17 13:32:19,287 templates.py:333 DEBUG name: versionsuffix, config:
== 2024-04-17 13:32:19,287 templates.py:333 DEBUG name: versionprefix, config:
== 2024-04-17 13:32:19,287 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='hapcut2', builddir='/eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0', github_account='hapcut2', installdir='/eb/software/HapCUT2/v1.3.3-GCC-12.3.0', module_name='HapCUT2/v1.3.3', name='HapCUT2', nameletter='H', nameletterlower='h', namelower='hapcut2', parallel='12', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='12.3.0', version='v1.3.3', version_major='v1', version_major_minor='v1.3', version_minor='3', versionprefix='', versionsuffix=''
== 2024-04-17 13:32:19,288 build_log.py:267 INFO ... (took < 1 sec)
== 2024-04-17 13:32:19,289 easyblock.py:3947 DEBUG Not skipping source step (skippable: True, skip: None, skipsteps: ['configure'], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False)
== 2024-04-17 13:32:19,289 build_log.py:267 INFO unpacking...
== 2024-04-17 13:32:19,290 easyblock.py:3956 INFO Starting source step
== 2024-04-17 13:32:19,290 easyconfig.py:1702 INFO Generating template values...
== 2024-04-17 13:32:19,290 templates.py:201 DEBUG config: HapCUT2 EasyConfig @ /eb/tmp/eb-rssr4be3/files_pr20380/h/HapCUT2/HapCUT2-v1.3.3-GCC-12.3.0.eb
== 2024-04-17 13:32:19,290 templates.py:231 DEBUG version found in easyconfig is v1.3.3
== 2024-04-17 13:32:19,290 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-04-17 13:32:19,290 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-04-17 13:32:19,290 templates.py:333 DEBUG name: name, config: HapCUT2
== 2024-04-17 13:32:19,290 templates.py:333 DEBUG name: parallel, config: 12
== 2024-04-17 13:32:19,290 templates.py:333 DEBUG name: version, config: v1.3.3
== 2024-04-17 13:32:19,290 templates.py:333 DEBUG name: versionsuffix, config:
== 2024-04-17 13:32:19,290 templates.py:333 DEBUG name: versionprefix, config:
== 2024-04-17 13:32:19,290 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='hapcut2', builddir='/eb/tmp/eb-build/HapCUT2/v1.3.3/GCC-12.3.0', github_account='hapcut2', installdir='/eb/software/HapCUT2/v1.3.3-GCC-12.3.0', module_name='HapCUT2/v1.3.3', name='HapCUT2', nameletter='H', nameletterlower='h', namelower='hapcut2', parallel='12', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='12.3.0', version='v1.3.3', version_major='v1', version_major_minor='v1.3', version_minor='3', versionprefix='', versionsuffix=''
== 2024-04-17 13:32:19,290 easyblock.py:3964 INFO Running method checksum_step part of step source
== 2024-04-17 13:32:19,290 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-04-17 13:32:19,293 filetools.py:1307 DEBUG Computed sha256 checksum for /eb/sources/h/HapCUT2/v1.3.3.tar.gz: 59b3e75f538ffb5cc586a6842049b52e92d7cfc9325bf1b9843185efe90abd89 (correct checksum: 4ff42519d7f9ed8159d41adc94bff7c600145424f5b501b1ece7930cfdd74e9f)
== 2024-04-17 13:32:19,321 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/tools/build_log.py:111 in caller_info): Checksum verification for /eb/sources/h/HapCUT2/v1.3.3.tar.gz using {'v1.3.3.tar.gz': '4ff42519d7f9ed8159d41adc94bff7c600145424f5b501b1ece7930cfdd74e9f'} failed. (at easybuild/framework/easyblock.py:2471 in checksum_step)
== 2024-04-17 13:32:19,321 build_log.py:267 INFO ... (took < 1 sec)
== 2024-04-17 13:32:19,322 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/software
== 2024-04-17 13:32:19,322 filetools.py:2013 INFO Removing lock /eb/software/.locks/_eb_software_HapCUT2_v1.3.3-GCC-12.3.0.lock...
== 2024-04-17 13:32:19,322 filetools.py:383 INFO Path /eb/software/.locks/_eb_software_HapCUT2_v1.3.3-GCC-12.3.0.lock successfully removed.
== 2024-04-17 13:32:19,322 filetools.py:2017 INFO Lock removed: /eb/software/.locks/_eb_software_HapCUT2_v1.3.3-GCC-12.3.0.lock
== 2024-04-17 13:32:19,322 easyblock.py:4291 WARNING build failed (first 300 chars): Checksum verification for /eb/sources/h/HapCUT2/v1.3.3.tar.gz using {'v1.3.3.tar.gz': '4ff42519d7f9ed8159d41adc94bff7c600145424f5b501b1ece7930cfdd74e9f'} failed.
== 2024-04-17 13:32:19,322 easyblock.py:328 INFO Closing log for application name HapCUT2 version v1.3.3