Skip to content

Instantly share code, notes, and snippets.

@bedroge

bedroge/Raven-1.8.1-GCC-11.2.0_partial.log

Created January 5, 2023 12:29
Star
Embed
What would you like to do?
Learn more about clone URLs
Download ZIP
(partial) EasyBuild log for failed build of /data/eb/tmp/eb-64v6x70e/files_pr15833/r/Raven/Raven-1.8.1-GCC-11.2.0.eb (PR(s) #15833)
Raw
Raven-1.8.1-GCC-11.2.0_partial.log
| ^
/data/eb/build/Raven/1.8.1/GCC-11.2.0/raven-1.8.1/RavenExe/src/main.cc:275:11: warning: C++ designated initializers only available with -std=c++20 or -std=gnu++20 [-Wpedantic]
275 | .num_rounds = num_polishing_rounds}
| ^
[15/26] Building CXX object _deps/edlib-build/CMakeFiles/edlib.dir/edlib/src/edlib.cpp.o
[16/26] Linking CXX static library lib/libedlib.a
[17/26] Building CXX object _deps/racon-build/CMakeFiles/racon.dir/src/polisher.cpp.o
[18/26] Building CXX object _deps/spoa-build/CMakeFiles/spoa.dir/src/graph.cpp.o
[19/26] Building CXX object _deps/ram-build/CMakeFiles/ram.dir/src/minimizer_engine.cpp.o
[20/26] Linking CXX static library _deps/ram-build/lib/libram.a
[21/26] Building CXX object _deps/spoa-build/CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o
[22/26] Building CXX object _deps/spoa-build/CMakeFiles/spoa.dir/src/simd_alignment_engine_dispatcher.cpp.o
[23/26] Linking CXX static library _deps/spoa-build/lib/libspoa.a
[24/26] Linking CXX static library _deps/racon-build/lib/libracon.a
[25/26] Linking CXX static library lib/libraven.a
[26/26] Linking CXX executable bin/raven
== 2023-01-05 13:28:58,117 build_log.py:265 INFO ... (took 11 secs)
== 2023-01-05 13:28:58,119 build_log.py:265 INFO testing...
== 2023-01-05 13:28:58,121 easyblock.py:3766 INFO Starting test step
== 2023-01-05 13:28:58,121 easyconfig.py:1686 INFO Generating template values...
== 2023-01-05 13:28:58,121 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='raven', builddir='/data/eb/build/Raven/1.8.1/GCC-11.2.0', cuda_cc_cmake='70', cuda_cc_semicolon_sep='7.0', cuda_cc_space_sep='7.0', cuda_compute_capabilities='7.0', cuda_sm_comma_sep='sm_70', cuda_sm_space_sep='sm_70', github_account='raven', installdir='/data/apps/software/Raven/1.8.1-GCC-11.2.0', module_name='Raven/1.8.1-GCC-11.2.0', name='Raven', nameletter='R', nameletterlower='r', namelower='raven', parallel='6', pymajver='3', pyminver='9', pyshortver='3.9', pyver='3.9.6', toolchain_name='GCC', toolchain_version='11.2.0', version='1.8.1', version_major='1', version_major_minor='1.8', version_minor='8', versionprefix='', versionsuffix=''
== 2023-01-05 13:28:58,121 easyblock.py:3774 INFO Running method test_step part of step test
== 2023-01-05 13:28:58,122 environment.py:91 INFO Environment variable CTEST_OUTPUT_ON_FAILURE set to True (previously undefined)
== 2023-01-05 13:28:58,122 build_log.py:265 INFO installing...
== 2023-01-05 13:28:58,123 easyblock.py:3766 INFO Starting install step
== 2023-01-05 13:28:58,123 easyconfig.py:1686 INFO Generating template values...
== 2023-01-05 13:28:58,124 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='raven', builddir='/data/eb/build/Raven/1.8.1/GCC-11.2.0', cuda_cc_cmake='70', cuda_cc_semicolon_sep='7.0', cuda_cc_space_sep='7.0', cuda_compute_capabilities='7.0', cuda_sm_comma_sep='sm_70', cuda_sm_space_sep='sm_70', github_account='raven', installdir='/data/apps/software/Raven/1.8.1-GCC-11.2.0', module_name='Raven/1.8.1-GCC-11.2.0', name='Raven', nameletter='R', nameletterlower='r', namelower='raven', parallel='6', pymajver='3', pyminver='9', pyshortver='3.9', pyver='3.9.6', toolchain_name='GCC', toolchain_version='11.2.0', version='1.8.1', version_major='1', version_major_minor='1.8', version_minor='8', versionprefix='', versionsuffix=''
== 2023-01-05 13:28:58,124 easyblock.py:3774 INFO Running method stage_install_step part of step install
== 2023-01-05 13:28:58,124 easyblock.py:3774 INFO Running method make_installdir part of step install
== 2023-01-05 13:28:58,124 easyblock.py:1072 INFO Found old directory /data/apps/software/Raven/1.8.1-GCC-11.2.0
== 2023-01-05 13:28:58,130 filetools.py:382 INFO Path /data/apps/software/Raven/1.8.1-GCC-11.2.0 successfully removed.
== 2023-01-05 13:28:58,130 easyblock.py:1080 INFO Removed old directory /data/apps/software/Raven/1.8.1-GCC-11.2.0
== 2023-01-05 13:28:58,131 filetools.py:1913 INFO Creating directory /data/apps/software/Raven/1.8.1-GCC-11.2.0 (parents: True, set_gid: False, sticky: False)
== 2023-01-05 13:28:58,131 easyblock.py:3774 INFO Running method install_step part of step install
== 2023-01-05 13:28:58,131 run.py:234 INFO running cmd: export CMAKE_BUILD_PARALLEL_LEVEL=6 && ninja -j 6 install
== 2023-01-05 13:28:58,149 run.py:646 INFO cmd "export CMAKE_BUILD_PARALLEL_LEVEL=6 && ninja -j 6 install" exited with exit code 0 and output:
[0/1] Install the project...
-- Install configuration: "Release"
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/libraven.a
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/libracon.a
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/libram.a
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/libspoa.a
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/bin/raven
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/raven.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/construct.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/serialization
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/serialization/binary.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/serialization/serialization.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/serialization/graph_repr.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/overlap_utils.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/all.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/assemble.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/polish.hpp
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/graph.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/graph/common.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/io.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/pile.h
-- Up-to-date: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include
-- Up-to-date: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/include/raven/export.h
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/cmake/raven/raven--targets.cmake
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/cmake/raven/raven--targets-release.cmake
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/cmake/raven/ravenConfig.cmake
-- Installing: /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/cmake/raven/ravenConfigVersion.cmake
== 2023-01-05 13:28:58,150 build_log.py:265 INFO taking care of extensions...
== 2023-01-05 13:28:58,152 easyblock.py:3766 INFO Starting extensions step
== 2023-01-05 13:28:58,152 easyconfig.py:1686 INFO Generating template values...
== 2023-01-05 13:28:58,152 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='raven', builddir='/data/eb/build/Raven/1.8.1/GCC-11.2.0', cuda_cc_cmake='70', cuda_cc_semicolon_sep='7.0', cuda_cc_space_sep='7.0', cuda_compute_capabilities='7.0', cuda_sm_comma_sep='sm_70', cuda_sm_space_sep='sm_70', github_account='raven', installdir='/data/apps/software/Raven/1.8.1-GCC-11.2.0', module_name='Raven/1.8.1-GCC-11.2.0', name='Raven', nameletter='R', nameletterlower='r', namelower='raven', parallel='6', pymajver='3', pyminver='9', pyshortver='3.9', pyver='3.9.6', toolchain_name='GCC', toolchain_version='11.2.0', version='1.8.1', version_major='1', version_major_minor='1.8', version_minor='8', versionprefix='', versionsuffix=''
== 2023-01-05 13:28:58,152 easyblock.py:3774 INFO Running method extensions_step part of step extensions
== 2023-01-05 13:28:58,243 filetools.py:1913 INFO Creating directory /data/eb/tmp/eb-64v6x70e/tmp9yixaw9n/all/Raven (parents: True, set_gid: False, sticky: False)
== 2023-01-05 13:28:58,243 easyblock.py:3582 INFO Module file /data/eb/tmp/eb-64v6x70e/tmp9yixaw9n/all/Raven/1.8.1-GCC-11.2.0.lua written: help([==[
Description
===========
Raven is a de novo genome assembler for long uncorrected reads.
More information
================
- Homepage: https://github.com/lbcb-sci/raven
Included extensions
===================
Raven-1.8.1
]==])
whatis([==[Description: Raven is a de novo genome assembler for long uncorrected reads.]==])
whatis([==[Homepage: https://github.com/lbcb-sci/raven]==])
whatis([==[URL: https://github.com/lbcb-sci/raven]==])
whatis([==[Extensions: Raven-1.8.1]==])
local root = "/data/apps/software/Raven/1.8.1-GCC-11.2.0"
conflict("Raven")
if not ( isloaded("GCC/11.2.0") ) then
load("GCC/11.2.0")
end
if not ( isloaded("Python/3.9.6-GCCcore-11.2.0") ) then
load("Python/3.9.6-GCCcore-11.2.0")
end
if not ( isloaded("zlib/1.2.11-GCCcore-11.2.0") ) then
load("zlib/1.2.11-GCCcore-11.2.0")
end
prepend_path("CMAKE_PREFIX_PATH", root)
prepend_path("CPATH", pathJoin(root, "include"))
prepend_path("LD_LIBRARY_PATH", pathJoin(root, "lib"))
prepend_path("LIBRARY_PATH", pathJoin(root, "lib"))
prepend_path("PATH", pathJoin(root, "bin"))
setenv("EBROOTRAVEN", root)
setenv("EBVERSIONRAVEN", "1.8.1")
setenv("EBDEVELRAVEN", pathJoin(root, "easybuild/Raven-1.8.1-GCC-11.2.0-easybuild-devel"))
prepend_path("PYTHONPATH", pathJoin(root, "lib/python3.9/site-packages"))
-- Built with EasyBuild version 4.6.2
setenv("EBEXTSLISTRAVEN", "Raven-1.8.1")
== 2023-01-05 13:28:58,244 filetools.py:1913 INFO Creating directory /data/eb/tmp/eb-64v6x70e/tmp9yixaw9n/bio/Raven (parents: True, set_gid: False, sticky: False)
== 2023-01-05 13:28:58,244 easyblock.py:3613 INFO Skipping devel module...
== 2023-01-05 13:28:58,244 filetools.py:337 INFO Symlinked 1.8.1-GCC-11.2.0.lua to /data/eb/tmp/eb-64v6x70e/tmp9yixaw9n/all/Raven/default
== 2023-01-05 13:28:58,244 module_generator.py:1487 INFO Module default version file written to point to /data/eb/tmp/eb-64v6x70e/tmp9yixaw9n/all/Raven/default
== 2023-01-05 13:28:58,374 environment.py:91 INFO Environment variable _ModuleTable002_ set to ci9tb2R1bGVmaWxlcy9MaW51eCIsICIvdXNyL21vZHVsZWZpbGVzL0NvcmUiLCAiL3Vzci9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsCn0sCnN5c3RlbUJhc2VNUEFUSCA9ICIvdXNyL21vZHVsZWZpbGVzL0xpbnV4Oi91c3IvbW9kdWxlZmlsZXMvQ29yZTovdXNyL2xtb2QvbG1vZC9tb2R1bGVmaWxlcy9Db3JlIiwKfQo= (previous value: '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')
== 2023-01-05 13:28:58,374 environment.py:91 INFO Environment variable __LMOD_REF_COUNT_MODULEPATH set to /data/apps/modules/all:1;/usr/modulefiles/Linux:1;/usr/modulefiles/Core:1;/usr/lmod/lmod/modulefiles/Core:1 (previous value: '/data/eb/tmp/eb-64v6x70e/tmp9yixaw9n/all:1;/data/apps/modules/all:1;/usr/modulefiles/Linux:1;/usr/modulefiles/Core:1;/usr/lmod/lmod/modulefiles/Core:1')
== 2023-01-05 13:28:58,374 environment.py:91 INFO Environment variable __LMOD_REF_COUNT__LMFILES_ set to /data/apps/modules/all/EasyBuild/4.6.2.lua:1 (previous value: '/data/apps/modules/all/EasyBuild/4.6.2.lua:1;/data/apps/modules/all/GCCcore/11.2.0.lua:1;/data/apps/modules/all/binutils/2.37-GCCcore-11.2.0.lua:1;/data/apps/modules/all/GCC/11.2.0.lua:1;/data/apps/modules/all/ncurses/6.2-GCCcore-11.2.0.lua:1;/data/apps/modules/all/bzip2/1.0.8-GCCcore-11.2.0.lua:1;/data/apps/modules/all/OpenSSL/1.1.lua:1;/data/apps/modules/all/cURL/7.78.0-GCCcore-11.2.0.lua:1;/data/apps/modules/all/XZ/5.2.5-GCCcore-11.2.0.lua:1;/data/apps/modules/all/libarchive/3.5.1-GCCcore-11.2.0.lua:1;/data/apps/modules/all/CMake/3.22.1-GCCcore-11.2.0.lua:1;/data/apps/modules/all/Ninja/1.10.2-GCCcore-11.2.0.lua:1;/data/apps/modules/all/libreadline/8.1-GCCcore-11.2.0.lua:1;/data/apps/modules/all/Tcl/8.6.11-GCCcore-11.2.0.lua:1;/data/apps/modules/all/SQLite/3.36-GCCcore-11.2.0.lua:1;/data/apps/modules/all/GMP/6.2.1-GCCcore-11.2.0.lua:1;/data/apps/modules/all/libffi/3.4.2-GCCcore-11.2.0.lua:1;/data/apps/modules/all/Python/3.9.6-GCCcore-11.2.0.lua:1;/data/apps/modules/all/zlib/1.2.11-GCCcore-11.2.0.lua:1')
== 2023-01-05 13:28:58,374 environment.py:91 INFO Environment variable MANPATH set to /usr/lmod/lmod/share/man:: (previous value: '/data/apps/software/zlib/1.2.11-GCCcore-11.2.0/share/man:/data/apps/software/Python/3.9.6-GCCcore-11.2.0/share/man:/data/apps/software/Python/3.9.6-GCCcore-11.2.0/man:/data/apps/software/libffi/3.4.2-GCCcore-11.2.0/share/man:/data/apps/software/SQLite/3.36-GCCcore-11.2.0/share/man:/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/share/man:/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/man:/data/apps/software/libreadline/8.1-GCCcore-11.2.0/share/man:/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0/share/man:/data/apps/software/XZ/5.2.5-GCCcore-11.2.0/share/man:/data/apps/software/cURL/7.78.0-GCCcore-11.2.0/share/man:/home/bob/.local/easybuild/software/OpenSSL/1.1/share/man:/data/apps/software/bzip2/1.0.8-GCCcore-11.2.0/man:/data/apps/software/ncurses/6.2-GCCcore-11.2.0/share/man:/data/apps/software/binutils/2.37-GCCcore-11.2.0/share/man:/data/apps/software/GCCcore/11.2.0/share/man:/usr/lmod/lmod/share/man::')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable __LMOD_REF_COUNT_CMAKE_PREFIX_PATH set to /data/apps/software/EasyBuild/4.6.2:1 (previous value: '/data/apps/software/zlib/1.2.11-GCCcore-11.2.0:1;/data/apps/software/Python/3.9.6-GCCcore-11.2.0:1;/data/apps/software/libffi/3.4.2-GCCcore-11.2.0:1;/data/apps/software/GMP/6.2.1-GCCcore-11.2.0:1;/data/apps/software/SQLite/3.36-GCCcore-11.2.0:1;/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0:1;/data/apps/software/libreadline/8.1-GCCcore-11.2.0:1;/data/apps/software/Ninja/1.10.2-GCCcore-11.2.0:1;/data/apps/software/CMake/3.22.1-GCCcore-11.2.0:1;/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0:1;/data/apps/software/XZ/5.2.5-GCCcore-11.2.0:1;/data/apps/software/cURL/7.78.0-GCCcore-11.2.0:1;/home/bob/.local/easybuild/software/OpenSSL/1.1:1;/data/apps/software/bzip2/1.0.8-GCCcore-11.2.0:1;/data/apps/software/ncurses/6.2-GCCcore-11.2.0:1;/data/apps/software/binutils/2.37-GCCcore-11.2.0:1;/data/apps/software/GCCcore/11.2.0:1;/data/apps/software/EasyBuild/4.6.2:1')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable __LMOD_REF_COUNT_PATH set to /data/apps/software/EasyBuild/4.6.2/bin:1;/home/bob/.local/bin:1;/home/bob/bin:1;/usr/local/sbin:1;/usr/local/bin:1;/usr/sbin:1;/usr/bin:1;/sbin:1;/bin:1;/usr/games:1;/usr/local/games:1;/snap/bin:2;/usr/local/go/bin:1 (previous value: '/data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin:1;/data/apps/software/SQLite/3.36-GCCcore-11.2.0/bin:1;/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/bin:1;/data/apps/software/Ninja/1.10.2-GCCcore-11.2.0/bin:1;/data/apps/software/CMake/3.22.1-GCCcore-11.2.0/bin:1;/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0/bin:1;/data/apps/software/XZ/5.2.5-GCCcore-11.2.0/bin:1;/data/apps/software/cURL/7.78.0-GCCcore-11.2.0/bin:1;/home/bob/.local/easybuild/software/OpenSSL/1.1/bin:1;/data/apps/software/bzip2/1.0.8-GCCcore-11.2.0/bin:1;/data/apps/software/ncurses/6.2-GCCcore-11.2.0/bin:1;/data/apps/software/binutils/2.37-GCCcore-11.2.0/bin:1;/data/apps/software/GCCcore/11.2.0/bin:1;/data/apps/software/EasyBuild/4.6.2/bin:1;/home/bob/.local/bin:1;/home/bob/bin:1;/usr/local/sbin:1;/usr/local/bin:1;/usr/sbin:1;/usr/bin:1;/sbin:1;/bin:1;/usr/games:1;/usr/local/games:1;/snap/bin:2;/usr/local/go/bin:1')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable _ModuleTable_Sz_ set to 2 (previous value: '16')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable __LMOD_REF_COUNT_LOADEDMODULES set to EasyBuild/4.6.2:1 (previous value: 'EasyBuild/4.6.2:1;GCCcore/11.2.0:1;binutils/2.37-GCCcore-11.2.0:1;GCC/11.2.0:1;ncurses/6.2-GCCcore-11.2.0:1;bzip2/1.0.8-GCCcore-11.2.0:1;OpenSSL/1.1:1;cURL/7.78.0-GCCcore-11.2.0:1;XZ/5.2.5-GCCcore-11.2.0:1;libarchive/3.5.1-GCCcore-11.2.0:1;CMake/3.22.1-GCCcore-11.2.0:1;Ninja/1.10.2-GCCcore-11.2.0:1;libreadline/8.1-GCCcore-11.2.0:1;Tcl/8.6.11-GCCcore-11.2.0:1;SQLite/3.36-GCCcore-11.2.0:1;GMP/6.2.1-GCCcore-11.2.0:1;libffi/3.4.2-GCCcore-11.2.0:1;Python/3.9.6-GCCcore-11.2.0:1;zlib/1.2.11-GCCcore-11.2.0:1')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable CMAKE_PREFIX_PATH set to /data/apps/software/EasyBuild/4.6.2 (previous value: '/data/apps/software/zlib/1.2.11-GCCcore-11.2.0:/data/apps/software/Python/3.9.6-GCCcore-11.2.0:/data/apps/software/libffi/3.4.2-GCCcore-11.2.0:/data/apps/software/GMP/6.2.1-GCCcore-11.2.0:/data/apps/software/SQLite/3.36-GCCcore-11.2.0:/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0:/data/apps/software/libreadline/8.1-GCCcore-11.2.0:/data/apps/software/Ninja/1.10.2-GCCcore-11.2.0:/data/apps/software/CMake/3.22.1-GCCcore-11.2.0:/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0:/data/apps/software/XZ/5.2.5-GCCcore-11.2.0:/data/apps/software/cURL/7.78.0-GCCcore-11.2.0:/home/bob/.local/easybuild/software/OpenSSL/1.1:/data/apps/software/bzip2/1.0.8-GCCcore-11.2.0:/data/apps/software/ncurses/6.2-GCCcore-11.2.0:/data/apps/software/binutils/2.37-GCCcore-11.2.0:/data/apps/software/GCCcore/11.2.0:/data/apps/software/EasyBuild/4.6.2')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable __LMOD_REF_COUNT_XDG_DATA_DIRS set to /usr/share/ubuntu:1;/usr/local/share:1;/usr/share:1;/var/lib/snapd/desktop:1 (previous value: '/data/apps/software/zlib/1.2.11-GCCcore-11.2.0/share:1;/data/apps/software/Python/3.9.6-GCCcore-11.2.0/share:1;/data/apps/software/libffi/3.4.2-GCCcore-11.2.0/share:1;/data/apps/software/GMP/6.2.1-GCCcore-11.2.0/share:1;/data/apps/software/SQLite/3.36-GCCcore-11.2.0/share:1;/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/share:1;/data/apps/software/libreadline/8.1-GCCcore-11.2.0/share:1;/data/apps/software/CMake/3.22.1-GCCcore-11.2.0/share:1;/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0/share:1;/data/apps/software/XZ/5.2.5-GCCcore-11.2.0/share:1;/data/apps/software/cURL/7.78.0-GCCcore-11.2.0/share:1;/home/bob/.local/easybuild/software/OpenSSL/1.1/share:1;/data/apps/software/ncurses/6.2-GCCcore-11.2.0/share:1;/data/apps/software/binutils/2.37-GCCcore-11.2.0/share:1;/data/apps/software/GCCcore/11.2.0/share:1;/usr/share/ubuntu:1;/usr/local/share:1;/usr/share:1;/var/lib/snapd/desktop:1')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable __LMOD_REF_COUNT_PYTHONPATH set to /data/apps/software/EasyBuild/4.6.2/lib/python3.10/site-packages:1 (previous value: '/data/apps/software/Python/3.9.6-GCCcore-11.2.0/easybuild/python:1')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable LOADEDMODULES set to EasyBuild/4.6.2 (previous value: 'EasyBuild/4.6.2:GCCcore/11.2.0:binutils/2.37-GCCcore-11.2.0:GCC/11.2.0:ncurses/6.2-GCCcore-11.2.0:bzip2/1.0.8-GCCcore-11.2.0:OpenSSL/1.1:cURL/7.78.0-GCCcore-11.2.0:XZ/5.2.5-GCCcore-11.2.0:libarchive/3.5.1-GCCcore-11.2.0:CMake/3.22.1-GCCcore-11.2.0:Ninja/1.10.2-GCCcore-11.2.0:libreadline/8.1-GCCcore-11.2.0:Tcl/8.6.11-GCCcore-11.2.0:SQLite/3.36-GCCcore-11.2.0:GMP/6.2.1-GCCcore-11.2.0:libffi/3.4.2-GCCcore-11.2.0:Python/3.9.6-GCCcore-11.2.0:zlib/1.2.11-GCCcore-11.2.0')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable __LMOD_REF_COUNT_MANPATH set to /usr/lmod/lmod/share/man:1 (previous value: '/data/apps/software/zlib/1.2.11-GCCcore-11.2.0/share/man:1;/data/apps/software/Python/3.9.6-GCCcore-11.2.0/share/man:1;/data/apps/software/Python/3.9.6-GCCcore-11.2.0/man:1;/data/apps/software/libffi/3.4.2-GCCcore-11.2.0/share/man:1;/data/apps/software/SQLite/3.36-GCCcore-11.2.0/share/man:1;/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/share/man:1;/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/man:1;/data/apps/software/libreadline/8.1-GCCcore-11.2.0/share/man:1;/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0/share/man:1;/data/apps/software/XZ/5.2.5-GCCcore-11.2.0/share/man:1;/data/apps/software/cURL/7.78.0-GCCcore-11.2.0/share/man:1;/home/bob/.local/easybuild/software/OpenSSL/1.1/share/man:1;/data/apps/software/bzip2/1.0.8-GCCcore-11.2.0/man:1;/data/apps/software/ncurses/6.2-GCCcore-11.2.0/share/man:1;/data/apps/software/binutils/2.37-GCCcore-11.2.0/share/man:1;/data/apps/software/GCCcore/11.2.0/share/man:1;/usr/lmod/lmod/share/man:1')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable _ModuleTable001_ set to 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 (previous value: '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')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable XDG_DATA_DIRS set to /usr/share/ubuntu:/usr/local/share:/usr/share:/var/lib/snapd/desktop (previous value: '/data/apps/software/zlib/1.2.11-GCCcore-11.2.0/share:/data/apps/software/Python/3.9.6-GCCcore-11.2.0/share:/data/apps/software/libffi/3.4.2-GCCcore-11.2.0/share:/data/apps/software/GMP/6.2.1-GCCcore-11.2.0/share:/data/apps/software/SQLite/3.36-GCCcore-11.2.0/share:/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/share:/data/apps/software/libreadline/8.1-GCCcore-11.2.0/share:/data/apps/software/CMake/3.22.1-GCCcore-11.2.0/share:/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0/share:/data/apps/software/XZ/5.2.5-GCCcore-11.2.0/share:/data/apps/software/cURL/7.78.0-GCCcore-11.2.0/share:/home/bob/.local/easybuild/software/OpenSSL/1.1/share:/data/apps/software/ncurses/6.2-GCCcore-11.2.0/share:/data/apps/software/binutils/2.37-GCCcore-11.2.0/share:/data/apps/software/GCCcore/11.2.0/share:/usr/share/ubuntu:/usr/local/share:/usr/share:/var/lib/snapd/desktop')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable PATH set to /data/apps/software/EasyBuild/4.6.2/bin:/home/bob/.local/bin:/home/bob/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/go/bin (previous value: '/data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin:/data/apps/software/SQLite/3.36-GCCcore-11.2.0/bin:/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/bin:/data/apps/software/Ninja/1.10.2-GCCcore-11.2.0/bin:/data/apps/software/CMake/3.22.1-GCCcore-11.2.0/bin:/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0/bin:/data/apps/software/XZ/5.2.5-GCCcore-11.2.0/bin:/data/apps/software/cURL/7.78.0-GCCcore-11.2.0/bin:/home/bob/.local/easybuild/software/OpenSSL/1.1/bin:/data/apps/software/bzip2/1.0.8-GCCcore-11.2.0/bin:/data/apps/software/ncurses/6.2-GCCcore-11.2.0/bin:/data/apps/software/binutils/2.37-GCCcore-11.2.0/bin:/data/apps/software/GCCcore/11.2.0/bin:/data/apps/software/EasyBuild/4.6.2/bin:/home/bob/.local/bin:/home/bob/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/go/bin')
== 2023-01-05 13:28:58,375 environment.py:91 INFO Environment variable MODULEPATH set to /data/apps/modules/all:/usr/modulefiles/Linux:/usr/modulefiles/Core:/usr/lmod/lmod/modulefiles/Core (previous value: '/data/eb/tmp/eb-64v6x70e/tmp9yixaw9n/all:/data/apps/modules/all:/usr/modulefiles/Linux:/usr/modulefiles/Core:/usr/lmod/lmod/modulefiles/Core')
== 2023-01-05 13:28:58,376 environment.py:91 INFO Environment variable _LMFILES_ set to /data/apps/modules/all/EasyBuild/4.6.2.lua (previous value: '/data/apps/modules/all/EasyBuild/4.6.2.lua:/data/apps/modules/all/GCCcore/11.2.0.lua:/data/apps/modules/all/binutils/2.37-GCCcore-11.2.0.lua:/data/apps/modules/all/GCC/11.2.0.lua:/data/apps/modules/all/ncurses/6.2-GCCcore-11.2.0.lua:/data/apps/modules/all/bzip2/1.0.8-GCCcore-11.2.0.lua:/data/apps/modules/all/OpenSSL/1.1.lua:/data/apps/modules/all/cURL/7.78.0-GCCcore-11.2.0.lua:/data/apps/modules/all/XZ/5.2.5-GCCcore-11.2.0.lua:/data/apps/modules/all/libarchive/3.5.1-GCCcore-11.2.0.lua:/data/apps/modules/all/CMake/3.22.1-GCCcore-11.2.0.lua:/data/apps/modules/all/Ninja/1.10.2-GCCcore-11.2.0.lua:/data/apps/modules/all/libreadline/8.1-GCCcore-11.2.0.lua:/data/apps/modules/all/Tcl/8.6.11-GCCcore-11.2.0.lua:/data/apps/modules/all/SQLite/3.36-GCCcore-11.2.0.lua:/data/apps/modules/all/GMP/6.2.1-GCCcore-11.2.0.lua:/data/apps/modules/all/libffi/3.4.2-GCCcore-11.2.0.lua:/data/apps/modules/all/Python/3.9.6-GCCcore-11.2.0.lua:/data/apps/modules/all/zlib/1.2.11-GCCcore-11.2.0.lua')
== 2023-01-05 13:28:58,376 modules.py:472 INFO $MODULEPATH set via list of module paths (w/ 'module use'): /data/eb/tmp/eb-64v6x70e/tmp9yixaw9n/all:/data/apps/modules/all:/usr/modulefiles/Linux:/usr/modulefiles/Core:/usr/lmod/lmod/modulefiles/Core
== 2023-01-05 13:28:58,817 environment.py:91 INFO Environment variable LD_LIBRARY_PATH set to /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib:/data/apps/software/Python/3.9.6-GCCcore-11.2.0/lib:/data/apps/software/libffi/3.4.2-GCCcore-11.2.0/lib64:/data/apps/software/GMP/6.2.1-GCCcore-11.2.0/lib:/data/apps/software/SQLite/3.36-GCCcore-11.2.0/lib:/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/lib:/data/apps/software/libreadline/8.1-GCCcore-11.2.0/lib:/data/apps/software/binutils/2.37-GCCcore-11.2.0/lib:/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0/lib:/data/apps/software/XZ/5.2.5-GCCcore-11.2.0/lib:/data/apps/software/cURL/7.78.0-GCCcore-11.2.0/lib:/home/bob/.local/easybuild/software/OpenSSL/1.1/lib:/data/apps/software/bzip2/1.0.8-GCCcore-11.2.0/lib:/data/apps/software/zlib/1.2.11-GCCcore-11.2.0/lib:/data/apps/software/ncurses/6.2-GCCcore-11.2.0/lib:/data/apps/software/GCCcore/11.2.0/lib64 (previous value: '/data/apps/software/Raven/1.8.1-GCC-11.2.0/lib:/data/apps/software/Python/3.9.6-GCCcore-11.2.0/lib:/data/apps/software/libffi/3.4.2-GCCcore-11.2.0/lib64:/data/apps/software/GMP/6.2.1-GCCcore-11.2.0/lib:/data/apps/software/SQLite/3.36-GCCcore-11.2.0/lib:/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/lib:/data/apps/software/libreadline/8.1-GCCcore-11.2.0/lib:/data/apps/software/binutils/2.37-GCCcore-11.2.0/lib')
== 2023-01-05 13:28:58,818 easyblock.py:2767 INFO Installing extensions
== 2023-01-05 13:28:58,840 easyconfig.py:462 INFO Performing quick parse to check for valid easyconfig file...
== 2023-01-05 13:28:58,842 environment.py:91 INFO Environment variable LMOD_QUIET set to 1 (previous value: '1')
== 2023-01-05 13:28:58,842 environment.py:91 INFO Environment variable LMOD_IGNORE_CACHE set to 1 (previous value: '1')
== 2023-01-05 13:28:58,842 environment.py:91 INFO Environment variable LMOD_REDIRECT set to no (previous value: 'no')
== 2023-01-05 13:28:58,842 environment.py:91 INFO Environment variable LMOD_EXTENDED_DEFAULT set to no (previous value: 'no')
== 2023-01-05 13:28:58,843 modules.py:299 INFO Full path for Lmod command is /usr/lmod/lmod/libexec/lmod, so using it
== 2023-01-05 13:28:58,843 modules.py:455 INFO Prepended list of module paths with path used by EasyBuild: /data/apps/modules/all
== 2023-01-05 13:28:58,844 easyconfig.py:471 INFO Obtained list of valid module classes: ['base', 'ai', 'astro', 'bio', 'cae', 'chem', 'compiler', 'data', 'debugger', 'devel', 'geo', 'ide', 'lang', 'lib', 'math', 'mpi', 'numlib', 'perf', 'quantum', 'phys', 'system', 'toolchain', 'tools', 'vis']
== 2023-01-05 13:28:58,845 easyconfig.py:1892 INFO Derived full easyblock module path for CMakeNinja: easybuild.easyblocks.generic.cmakeninja
== 2023-01-05 13:28:58,845 easyconfig.py:1938 INFO Successfully obtained class 'CMakeNinja' for easyblock 'CMakeNinja' (software name 'Raven')
== 2023-01-05 13:28:58,845 easyconfig.py:703 INFO Parsing easyconfig file None with rawcontent: easyblock = "CMakeNinja"
name = "Raven"
version = "1.8.1"
homepage = "https://github.com/lbcb-sci/raven"
description = "Raven is a de novo genome assembler for long uncorrected reads."
toolchain = {'name': 'GCC', 'version': '11.2.0'}
source_urls = ["https://github.com/lbcb-sci/raven/archive/refs/tags/"]
sources = ["%(version)s.tar.gz"]
checksums = ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06']
builddependencies = [
('CMake', '3.22.1'),
('Ninja', '1.10.2'),
]
preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && "
configopts = '-DRAVEN_BUILD_EXE=1 -G Ninja '
configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
dependencies = [
('Python', '3.9.6'),
('zlib', '1.2.11'),
]
exts_defaultclass = 'PythonPackage'
exts_default_options = {
'download_dep_fail': True,
'use_pip': True,
}
exts_list = [
(name, version, {
'modulename': 'ravenpy',
'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'],
'sources': ['%(version)s.tar.gz'],
'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'],
}),
]
modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
sanity_check_paths = {
'files': ['bin/raven'],
'dirs': []
}
sanity_check_commands = [
"pip check",
"raven --help"
]
moduleclass = "bio"
== 2023-01-05 13:28:58,846 parser.py:137 INFO Type checking of easyconfig parameter values passed!
== 2023-01-05 13:28:58,846 easyconfig.py:683 INFO setting easyconfig parameter builddependencies: value [('CMake', '3.22.1'), ('Ninja', '1.10.2')] (type: <class 'list'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter checksums: value ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'] (type: <class 'list'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter configopts: value -DRAVEN_BUILD_EXE=1 -G Ninja -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python (type: <class 'str'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter dependencies: value [('Python', '3.9.6'), ('zlib', '1.2.11')] (type: <class 'list'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter description: value Raven is a de novo genome assembler for long uncorrected reads. (type: <class 'str'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter easyblock: value CMakeNinja (type: <class 'str'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter exts_default_options: value {'download_dep_fail': True, 'use_pip': True} (type: <class 'dict'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter exts_defaultclass: value PythonPackage (type: <class 'str'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter exts_list: value [('Raven', '1.8.1', {'modulename': 'ravenpy', 'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'], 'sources': ['%(version)s.tar.gz'], 'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06']})] (type: <class 'list'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter homepage: value https://github.com/lbcb-sci/raven (type: <class 'str'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter modextrapaths: value {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} (type: <class 'dict'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter moduleclass: value bio (type: <class 'str'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter name: value Raven (type: <class 'str'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter preinstallopts: value export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && (type: <class 'str'>)
== 2023-01-05 13:28:58,847 easyconfig.py:683 INFO setting easyconfig parameter sanity_check_commands: value ['pip check', 'raven --help'] (type: <class 'list'>)
== 2023-01-05 13:28:58,848 easyconfig.py:683 INFO setting easyconfig parameter sanity_check_paths: value {'files': ['bin/raven'], 'dirs': []} (type: <class 'dict'>)
== 2023-01-05 13:28:58,848 easyconfig.py:683 INFO setting easyconfig parameter source_urls: value ['https://github.com/lbcb-sci/raven/archive/refs/tags/'] (type: <class 'list'>)
== 2023-01-05 13:28:58,848 easyconfig.py:683 INFO setting easyconfig parameter sources: value ['%(version)s.tar.gz'] (type: <class 'list'>)
== 2023-01-05 13:28:58,848 easyconfig.py:683 INFO setting easyconfig parameter toolchain: value {'name': 'GCC', 'version': '11.2.0'} (type: <class 'dict'>)
== 2023-01-05 13:28:58,848 easyconfig.py:683 INFO setting easyconfig parameter version: value 1.8.1 (type: <class 'str'>)
== 2023-01-05 13:28:58,848 easyconfig.py:745 INFO Parsing dependency specifications...
== 2023-01-05 13:28:58,848 easyconfig.py:1686 INFO Generating template values...
== 2023-01-05 13:28:58,850 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='raven', cuda_cc_cmake='70', cuda_cc_semicolon_sep='7.0', cuda_cc_space_sep='7.0', cuda_compute_capabilities='7.0', cuda_sm_comma_sep='sm_70', cuda_sm_space_sep='sm_70', github_account='raven', name='Raven', nameletter='R', nameletterlower='r', namelower='raven', pymajver='3', pyminver='9', pyshortver='3.9', pyver='3.9.6', toolchain_name='GCC', toolchain_version='11.2.0', version='1.8.1', version_major='1', version_major_minor='1.8', version_minor='8', versionprefix='', versionsuffix=''
== 2023-01-05 13:28:59,024 modules.py:626 INFO Checking whether CMake/3.22.1-GCC-11.2.0 exists...
== 2023-01-05 13:28:59,024 modules.py:647 INFO Module CMake/3.22.1-GCC-11.2.0 not found via module avail/show, checking whether it is a wrapper
== 2023-01-05 13:28:59,024 modules.py:654 INFO Result for existence check of CMake/3.22.1-GCC-11.2.0 module: False
== 2023-01-05 13:28:59,024 easyconfig.py:2177 INFO Found loaded index for /data/apps/software/EasyBuild/4.6.2/easybuild/easyconfigs
== 2023-01-05 13:28:59,025 easyconfig.py:2177 INFO Found loaded index for /data/eb/tmp/eb-64v6x70e/files_pr15833
== 2023-01-05 13:28:59,025 easyconfig.py:2353 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'CMake', 'version': '3.22.1', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '11.2.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.2.0'}
== 2023-01-05 13:28:59,025 modules.py:626 INFO Checking whether Ninja/1.10.2-GCC-11.2.0 exists...
== 2023-01-05 13:28:59,025 modules.py:647 INFO Module Ninja/1.10.2-GCC-11.2.0 not found via module avail/show, checking whether it is a wrapper
== 2023-01-05 13:28:59,025 modules.py:654 INFO Result for existence check of Ninja/1.10.2-GCC-11.2.0 module: False
== 2023-01-05 13:28:59,026 easyconfig.py:2177 INFO Found loaded index for /data/apps/software/EasyBuild/4.6.2/easybuild/easyconfigs
== 2023-01-05 13:28:59,026 easyconfig.py:2177 INFO Found loaded index for /data/eb/tmp/eb-64v6x70e/files_pr15833
== 2023-01-05 13:28:59,026 easyconfig.py:2353 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Ninja', 'version': '1.10.2', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '11.2.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.2.0'}
== 2023-01-05 13:28:59,026 modules.py:626 INFO Checking whether Python/3.9.6-GCC-11.2.0 exists...
== 2023-01-05 13:28:59,026 modules.py:647 INFO Module Python/3.9.6-GCC-11.2.0 not found via module avail/show, checking whether it is a wrapper
== 2023-01-05 13:28:59,027 modules.py:654 INFO Result for existence check of Python/3.9.6-GCC-11.2.0 module: False
== 2023-01-05 13:28:59,027 easyconfig.py:2177 INFO Found loaded index for /data/apps/software/EasyBuild/4.6.2/easybuild/easyconfigs
== 2023-01-05 13:28:59,027 easyconfig.py:2177 INFO Found loaded index for /data/eb/tmp/eb-64v6x70e/files_pr15833
== 2023-01-05 13:28:59,027 easyconfig.py:2353 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.9.6', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '11.2.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.2.0'}
== 2023-01-05 13:28:59,027 modules.py:626 INFO Checking whether zlib/1.2.11-GCC-11.2.0 exists...
== 2023-01-05 13:28:59,027 modules.py:647 INFO Module zlib/1.2.11-GCC-11.2.0 not found via module avail/show, checking whether it is a wrapper
== 2023-01-05 13:28:59,028 modules.py:654 INFO Result for existence check of zlib/1.2.11-GCC-11.2.0 module: False
== 2023-01-05 13:28:59,028 easyconfig.py:2177 INFO Found loaded index for /data/apps/software/EasyBuild/4.6.2/easybuild/easyconfigs
== 2023-01-05 13:28:59,028 easyconfig.py:2177 INFO Found loaded index for /data/eb/tmp/eb-64v6x70e/files_pr15833
== 2023-01-05 13:28:59,028 easyconfig.py:2353 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'zlib', 'version': '1.2.11', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '11.2.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.2.0'}
== 2023-01-05 13:28:59,030 pythonpackage.py:338 INFO Using pip with --no-deps option
== 2023-01-05 13:28:59,030 environment.py:91 INFO Environment variable XDG_CACHE_HOME set to /data/eb/tmp/eb-64v6x70e (previously undefined)
== 2023-01-05 13:28:59,030 pythonpackage.py:355 INFO Using /data/eb/tmp/eb-64v6x70e as pip cache directory
== 2023-01-05 13:28:59,030 pythonpackage.py:370 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command
== 2023-01-05 13:28:59,090 easyblock.py:1794 INFO Installing extensions sequentially...
== 2023-01-05 13:28:59,090 easyblock.py:1800 INFO Starting extension Raven
== 2023-01-05 13:28:59,090 build_log.py:265 INFO installing extension Raven 1.8.1 (1/1)...
== 2023-01-05 13:28:59,154 modules.py:626 INFO Checking whether GCC/11.2.0 exists...
== 2023-01-05 13:28:59,154 modules.py:633 INFO Module GCC/11.2.0 not found in list of available modules, checking via 'module show'...
== 2023-01-05 13:28:59,287 modules.py:654 INFO Result for existence check of GCC/11.2.0 module: True
== 2023-01-05 13:28:59,287 toolchain.py:760 INFO List of toolchain dependency modules and toolchain definition match!
== 2023-01-05 13:28:59,290 compiler.py:361 INFO _set_optimal_architecture: using march=native as optarch for x86_64.
== 2023-01-05 13:28:59,292 environment.py:91 INFO Environment variable CC set to gcc (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable EBVARCC set to gcc (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable CXX set to g++ (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable EBVARCXX set to g++ (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable F77 set to gfortran (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable EBVARF77 set to gfortran (previously undefined)
== 2023-01-05 13:28:59,294 environment.py:91 INFO Environment variable F90 set to gfortran (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable EBVARF90 set to gfortran (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable FC set to gfortran (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable EBVARFC set to gfortran (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable FLIBS set to -lgfortran (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable LDFLAGS set to -L/data/apps/software/GCCcore/11.2.0/lib64 -L/data/apps/software/GCCcore/11.2.0/lib (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable EBVARLDFLAGS set to -L/data/apps/software/GCCcore/11.2.0/lib64 -L/data/apps/software/GCCcore/11.2.0/lib (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable LIBS set to -lm -lpthread (previously undefined)
== 2023-01-05 13:28:59,295 environment.py:91 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined)
== 2023-01-05 13:28:59,296 environment.py:91 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined)
== 2023-01-05 13:28:59,296 environment.py:91 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined)
== 2023-01-05 13:28:59,296 environment.py:91 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,296 environment.py:91 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined)
== 2023-01-05 13:28:59,296 filetools.py:525 INFO Command python found at /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python
== 2023-01-05 13:28:59,296 pythonpackage.py:408 INFO Python command being used: /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python
== 2023-01-05 13:28:59,296 run.py:234 INFO running cmd: /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))'
== 2023-01-05 13:28:59,371 run.py:234 INFO running cmd: /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))'
== 2023-01-05 13:28:59,402 filetools.py:1913 INFO Creating directory /data/eb/build/Raven/1.8.1/GCC-11.2.0/Raven (parents: True, set_gid: False, sticky: False)
== 2023-01-05 13:28:59,402 run.py:234 INFO running cmd: tar xzf /data/eb/sources/r/Raven/1.8.1.tar.gz
== 2023-01-05 13:28:59,422 build_log.py:265 INFO configuring...
== 2023-01-05 13:28:59,424 environment.py:91 INFO Environment variable PYTHONNOUSERSITE set to 1 (previously undefined)
== 2023-01-05 13:28:59,424 run.py:234 INFO running cmd: /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])'
== 2023-01-05 13:28:59,452 pythonpackage.py:595 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.9.6
== 2023-01-05 13:28:59,452 pythonpackage.py:609 INFO Python's value for $LDSHARED ('x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 ') doesn't use current $CC value ('gcc'), fixing
== 2023-01-05 13:28:59,452 environment.py:91 INFO Environment variable LDSHARED set to gcc -shared (previously undefined)
== 2023-01-05 13:28:59,452 run.py:234 INFO running cmd: /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python -V; /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python -c 'import sys; print(sys.executable, sys.path)'
== 2023-01-05 13:28:59,476 build_log.py:265 INFO building...
== 2023-01-05 13:28:59,478 build_log.py:265 INFO testing...
== 2023-01-05 13:28:59,479 build_log.py:265 INFO installing...
== 2023-01-05 13:28:59,480 filetools.py:1913 INFO Creating directory /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/python3.9/site-packages (parents: True, set_gid: False, sticky: False)
== 2023-01-05 13:28:59,481 environment.py:91 INFO Environment variable PYTHONPATH set to /data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/python3.9/site-packages:/data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/python3.9/site-packages:/data/apps/software/Python/3.9.6-GCCcore-11.2.0/easybuild/python (previous value: '/data/apps/software/Raven/1.8.1-GCC-11.2.0/lib/python3.9/site-packages:/data/apps/software/Python/3.9.6-GCCcore-11.2.0/easybuild/python')
== 2023-01-05 13:28:59,481 environment.py:91 INFO Environment variable PATH set to /data/apps/software/Raven/1.8.1-GCC-11.2.0/bin:/data/apps/software/Raven/1.8.1-GCC-11.2.0/bin:/data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin:/data/apps/software/SQLite/3.36-GCCcore-11.2.0/bin:/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/bin:/data/apps/software/binutils/2.37-GCCcore-11.2.0/bin:/data/apps/software/Ninja/1.10.2-GCCcore-11.2.0/bin:/data/apps/software/CMake/3.22.1-GCCcore-11.2.0/bin:/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0/bin:/data/apps/software/XZ/5.2.5-GCCcore-11.2.0/bin:/data/apps/software/cURL/7.78.0-GCCcore-11.2.0/bin:/home/bob/.local/easybuild/software/OpenSSL/1.1/bin:/data/apps/software/bzip2/1.0.8-GCCcore-11.2.0/bin:/data/apps/software/ncurses/6.2-GCCcore-11.2.0/bin:/data/apps/software/GCCcore/11.2.0/bin:/data/apps/software/EasyBuild/4.6.2/bin:/home/bob/.local/bin:/home/bob/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/go/bin (previous value: '/data/apps/software/Raven/1.8.1-GCC-11.2.0/bin:/data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin:/data/apps/software/SQLite/3.36-GCCcore-11.2.0/bin:/data/apps/software/Tcl/8.6.11-GCCcore-11.2.0/bin:/data/apps/software/binutils/2.37-GCCcore-11.2.0/bin:/data/apps/software/Ninja/1.10.2-GCCcore-11.2.0/bin:/data/apps/software/CMake/3.22.1-GCCcore-11.2.0/bin:/data/apps/software/libarchive/3.5.1-GCCcore-11.2.0/bin:/data/apps/software/XZ/5.2.5-GCCcore-11.2.0/bin:/data/apps/software/cURL/7.78.0-GCCcore-11.2.0/bin:/home/bob/.local/easybuild/software/OpenSSL/1.1/bin:/data/apps/software/bzip2/1.0.8-GCCcore-11.2.0/bin:/data/apps/software/ncurses/6.2-GCCcore-11.2.0/bin:/data/apps/software/GCCcore/11.2.0/bin:/data/apps/software/EasyBuild/4.6.2/bin:/home/bob/.local/bin:/home/bob/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/go/bin')
== 2023-01-05 13:28:59,481 pythonpackage.py:212 INFO Determining pip version...
== 2023-01-05 13:28:59,481 run.py:234 INFO running cmd: /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python -m pip --version
== 2023-01-05 13:29:00,003 pythonpackage.py:220 INFO Found pip version: 21.2.2
== 2023-01-05 13:29:00,003 pythonpackage.py:481 INFO Found pip version 21.2.2, OK
== 2023-01-05 13:29:00,003 run.py:234 INFO running cmd: export CMAKE_BUILD_PARALLEL_LEVEL=6 && /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python -m pip install --prefix=/data/apps/software/Raven/1.8.1-GCC-11.2.0 --no-deps --ignore-installed --no-index --no-build-isolation .
== 2023-01-05 13:29:37,779 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd "export CMAKE_BUILD_PARALLEL_LEVEL=6 && /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python -m pip install --prefix=/data/apps/software/Raven/1.8.1-GCC-11.2.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output:
Processing /data/eb/build/Raven/1.8.1/GCC-11.2.0/Raven/raven-1.8.1
DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
Preparing wheel metadata: started
Preparing wheel metadata: finished with status 'done'
Building wheels for collected packages: ravenpy
Building wheel for ravenpy (PEP 517): started
Building wheel for ravenpy (PEP 517): finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python /data/apps/software/Python/3.9.6-GCCcore-11.2.0/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /data/eb/tmp/eb-64v6x70e/tmpl8j95uho
cwd: /data/eb/tmp/eb-64v6x70e/pip-req-build-nck38j2k
Complete output (139 lines):
running bdist_wheel
running build
running build_ext
[ravenpy::setup.py] extdir: /data/eb/tmp/eb-64v6x70e/pip-req-build-nck38j2k/build/lib.linux-x86_64-3.9
[ravenpy::setup.py] /data/eb/tmp/eb-64v6x70e/pip-req-build-nck38j2k/build/lib.linux-x86_64-3.9/ravenpy_build/lib/ravenpy.cpython-39-x86_64-linux-gnu.so -> /data/eb/tmp/eb-64v6x70e/pip-req-build-nck38j2k/build/lib.linux-x86_64-3.9/ravenpy.cpython-39-x86_64-linux-gnu.so
-- The CXX compiler identification is GNU 11.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /data/apps/software/GCCcore/11.2.0/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found ZLIB: /data/apps/software/zlib/1.2.11-GCCcore-11.2.0/lib/libz.so (found suitable version "1.2.11", minimum required is "1.2.8")
CMake Deprecation Warning at build/lib.linux-x86_64-3.9/ravenpy_build/_deps/cereal-src/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
CMake Warning (dev) at build/lib.linux-x86_64-3.9/ravenpy_build/_deps/cereal-src/CMakeLists.txt:2 (project):
Policy CMP0048 is not set: project() command manages VERSION variables.
Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The following variable(s) would be set to empty:
PROJECT_VERSION
PROJECT_VERSION_MAJOR
PROJECT_VERSION_MINOR
PROJECT_VERSION_PATCH
This warning is for project developers. Use -Wno-dev to suppress it.
-- The C compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /data/apps/software/GCCcore/11.2.0/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Could NOT find Boost (missing: Boost_INCLUDE_DIR serialization)
-- optional.cpp
-- variant.cpp
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
Setting warning flags
-- Performing Test WOLD_STYLE_CAST
-- Performing Test WOLD_STYLE_CAST - Success
-- Performing Test WSHADOW
-- Performing Test WSHADOW - Success
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- pybind11 v2.9.1
-- Found PythonInterp: /usr/bin/python3.10 (found version "3.10.6")
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Configuring done
CMake Warning (dev) at build/lib.linux-x86_64-3.9/ravenpy_build/_deps/edlib-src/CMakeLists.txt:54 (add_library):
Policy CMP0063 is not set: Honor visibility properties for all target
types. Run "cmake --help-policy CMP0063" for policy details. Use the
cmake_policy command to set the policy and suppress this warning.
Target "edlib" of type "STATIC_LIBRARY" has the following visibility
properties set for CXX:
CXX_VISIBILITY_PRESET
VISIBILITY_INLINES_HIDDEN
For compatibility CMake is not honoring them for this target.
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at build/lib.linux-x86_64-3.9/ravenpy_build/_deps/edlib-src/CMakeLists.txt:81 (add_executable):
Policy CMP0063 is not set: Honor visibility properties for all target
types. Run "cmake --help-policy CMP0063" for policy details. Use the
cmake_policy command to set the policy and suppress this warning.
Target "runTests" of type "EXECUTABLE" has the following visibility
properties set for CXX:
VISIBILITY_INLINES_HIDDEN
For compatibility CMake is not honoring them for this target.
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at build/lib.linux-x86_64-3.9/ravenpy_build/_deps/edlib-src/CMakeLists.txt:89 (add_executable):
Policy CMP0063 is not set: Honor visibility properties for all target
types. Run "cmake --help-policy CMP0063" for policy details. Use the
cmake_policy command to set the policy and suppress this warning.
Target "edlib-aligner" of type "EXECUTABLE" has the following visibility
properties set for CXX:
VISIBILITY_INLINES_HIDDEN
For compatibility CMake is not honoring them for this target.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Generating done
-- Build files have been written to: /data/eb/tmp/eb-64v6x70e/pip-req-build-nck38j2k/build/lib.linux-x86_64-3.9/ravenpy_build
[1/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/common.cc.o
[2/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/graph.cc.o
[3/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/io.cc.o
[4/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/overlap_utils.cc.o
[5/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/graph_repr.cc.o
[6/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/binary.cc.o
[7/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/pile.cc.o
[8/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/polish.cc.o
[9/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/assemble.cc.o
[10/26] Building CXX object _deps/racon-build/CMakeFiles/racon.dir/src/overlap.cpp.o
[11/26] Building CXX object CMakeFiles/raven.dir/RavenLib/src/construct.cc.o
/data/eb/tmp/eb-64v6x70e/pip-req-build-nck38j2k/RavenLib/src/construct.cc: In function void raven::ResolveChimericSequences(const std::shared_ptr<thread_pool::ThreadPool>&, const std::vector<std::unique_ptr<raven::Pile> >&, std::vector<std::vector<biosoup::Overlap> >&, const std::vector<std::unique_ptr<biosoup::NucleicAcid> >&):
/data/eb/tmp/eb-64v6x70e/pip-req-build-nck38j2k/RavenLib/src/construct.cc:192:63: warning: unused parameter sequences [-Wunused-parameter]
192 | const std::vector<std::unique_ptr<biosoup::NucleicAcid>>& sequences) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
[12/26] Building CXX object _deps/racon-build/CMakeFiles/racon.dir/src/window.cpp.o
[13/26] Building CXX object _deps/spoa-build/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o
[14/26] Building CXX object _deps/edlib-build/CMakeFiles/edlib.dir/edlib/src/edlib.cpp.o
[15/26] Linking CXX static library lib/libedlib.a
[16/26] Building CXX object _deps/racon-build/CMakeFiles/racon.dir/src/polisher.cpp.o
[17/26] Building CXX object _deps/spoa-build/CMakeFiles/spoa.dir/src/graph.cpp.o
[18/26] Building CXX object _deps/spoa-build/CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o
[19/26] Building CXX object _deps/ram-build/CMakeFiles/ram.dir/src/minimizer_engine.cpp.o
[20/26] Linking CXX static library _deps/ram-build/lib/libram.a
[21/26] Building CXX object _deps/spoa-build/CMakeFiles/spoa.dir/src/simd_alignment_engine_dispatcher.cpp.o
[22/26] Linking CXX static library _deps/spoa-build/lib/libspoa.a
[23/26] Linking CXX static library _deps/racon-build/lib/libracon.a
[24/26] Linking CXX static library lib/libraven.a
[25/26] Building CXX object CMakeFiles/ravenpy.dir/PythonLib/src/ravenpy.cc.o
[26/26] Linking CXX shared module lib/ravenpy.cpython-310-x86_64-linux-gnu.so
error: [Errno 2] No such file or directory: '/data/eb/tmp/eb-64v6x70e/pip-req-build-nck38j2k/build/lib.linux-x86_64-3.9/ravenpy_build/lib/ravenpy.cpython-39-x86_64-linux-gnu.so'
----------------------------------------
ERROR: Failed building wheel for ravenpy
Failed to build ravenpy
ERROR: Could not build wheels for ravenpy which use PEP 517 and cannot be installed directly
(at easybuild/tools/run.py:641 in parse_cmd_output)
== 2023-01-05 13:29:37,782 build_log.py:265 INFO ... (took 38 secs)
== 2023-01-05 13:29:37,785 build_log.py:265 INFO ... (took 39 secs)
== 2023-01-05 13:29:37,788 filetools.py:2014 INFO Removing lock /data/apps/software/.locks/_data_apps_software_Raven_1.8.1-GCC-11.2.0.lock...
== 2023-01-05 13:29:37,789 filetools.py:382 INFO Path /data/apps/software/.locks/_data_apps_software_Raven_1.8.1-GCC-11.2.0.lock successfully removed.
== 2023-01-05 13:29:37,790 filetools.py:2018 INFO Lock removed: /data/apps/software/.locks/_data_apps_software_Raven_1.8.1-GCC-11.2.0.lock
== 2023-01-05 13:29:37,790 easyblock.py:4097 WARNING build failed (first 300 chars): cmd "export CMAKE_BUILD_PARALLEL_LEVEL=6 && /data/apps/software/Python/3.9.6-GCCcore-11.2.0/bin/python -m pip install --prefix=/data/apps/software/Raven/1.8.1-GCC-11.2.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output:
Processing /data/eb/buil
== 2023-01-05 13:29:37,790 easyblock.py:319 INFO Closing log for application name Raven version 1.8.1
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment