easybuild-easyconfigs
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Published
20 hours ago •
easybuilders
easybuilders
This PR provides Easyconfigs for GenomeSTRiP 2.00.1958 and some dependencies. Perl EasyBlock issue reported #10552. It fixes multi-version java dependency #10557
Travis test report: 2/2 runs failed - see https://travis-ci.org/easybuilders/easybuild-easyconfigs/builds/682782186
Only showing partial log for 1st failed test suite run 22086.1; full log at https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/682782187
...
FAIL: test__parse_easyconfig_picard-2.6.0-Java-11.eb (test.easyconfigs.easyconfigs.EasyConfigTest)
Test for parsing of easyconfig picard-2.6.0-Java-11.eb
----------------------------------------------------------------------
Traceback (most recent call last):
File "<string>", line 1, in innertest
File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 850, in template_easyconfig_test
self.assertFalse(redefined_keys, redefined_keys_error_msg)
AssertionError: There should be no redefined easyconfig parameters, found 1: sources (2)
======================================================================
FAIL: test_changed_files_pull_request (test.easyconfigs.easyconfigs.EasyConfigTest)
Specific checks only done for the (easyconfig) files that were changed in a pull request.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 763, in test_changed_files_pull_request
self.check_https(changed_ecs)
File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 688, in check_https
self.assertFalse(failing_checks, '\n'.join(failing_checks))
AssertionError: Found http:// URL in GenomeSTRiP-2.00.1958-GCCcore-8.3.0-Java-11.eb, should be https:// : http://www.broadinstitute.org/software/genomestrip
Found http:// URL in picard-2.6.0-Java-11.eb, should be https:// : http://sourceforge.net/projects/picard
Found http:// URL in tabix-0.2.6-GCCcore-8.3.0.eb, should be https:// : http://sourceforge.net/projects/samtools/files/
----------------------------------------------------------------------
Ran 9794 tests in 540.708s
FAILED (failures=2)
ERROR: Not all tests were successful.
- 22086.2 - errored => https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/682782188
*bleep, bloop, I'm just a bot (boegelbot v20180813.01)*Please talk to my owner @boegel if you notice you me acting stupid),or submit a pull request to https://github.com/boegel/boegelbot fix the problem.
Travis test report: 2/2 runs failed - see https://travis-ci.org/easybuilders/easybuild-easyconfigs/builds/682820491
Only showing partial log for 1st failed test suite run 22097.1; full log at https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/682820493
...
FAIL: test__parse_easyconfig_picard-2.6.0-Java-11.eb (test.easyconfigs.easyconfigs.EasyConfigTest)
Test for parsing of easyconfig picard-2.6.0-Java-11.eb
----------------------------------------------------------------------
Traceback (most recent call last):
File "<string>", line 1, in innertest
File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 850, in template_easyconfig_test
self.assertFalse(redefined_keys, redefined_keys_error_msg)
AssertionError: There should be no redefined easyconfig parameters, found 1: sources (2)
----------------------------------------------------------------------
Ran 9794 tests in 531.089s
FAILED (failures=1)
ERROR: Not all tests were successful.
- 22097.2 - errored => https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/682820495
*bleep, bloop, I'm just a bot (boegelbot v20180813.01)*Please talk to my owner @boegel if you notice you me acting stupid),or submit a pull request to https://github.com/boegel/boegelbot fix the problem.
Travis test report: 2/2 runs failed - see https://travis-ci.org/easybuilders/easybuild-easyconfigs/builds/684076820
Only showing partial log for 1st failed test suite run 22161.1; full log at https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/684076821
...
File "/home/travis/virtualenv/python2.7.15/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
File "/home/travis/virtualenv/python2.7.15/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: picard/2.6.0-Java-11 (no easyconfig file or existing module found)'
======================================================================
ERROR: test_sanity_check_paths (test.easyconfigs.easyconfigs.EasyConfigTest)
Make sure specified sanity check paths adher to the requirements.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 492, in test_sanity_check_paths
self.process_all_easyconfigs()
File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 120, in process_all_easyconfigs
EasyConfigTest.ordered_specs = resolve_dependencies(EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
File "/home/travis/virtualenv/python2.7.15/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
File "/home/travis/virtualenv/python2.7.15/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: picard/2.6.0-Java-11 (no easyconfig file or existing module found)'
----------------------------------------------------------------------
Ran 9816 tests in 384.809s
FAILED (errors=4)
ERROR: Not all tests were successful.
travis_time:end:1063a852:start=1588813668514491280,finish=1588814055436012749,duration=386921521469,event=script
[0K[31;1mThe command "python -O -m test.easyconfigs.suite" exited with 2.[0m
travis_time:start:36a8d5e4
[0K$ unset PYTHONPATH
travis_time:end:36a8d5e4:start=1588814055439950204,finish=1588814055442281368,duration=2331164,event=script
[0K[32;1mThe command "unset PYTHONPATH" exited with 0.[0m
travis_time:start:052eda10
[0K$ cd $HOME; pip install $TRAVIS_BUILD_DIR
[33mDEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.[0m
Processing ./build/easybuilders/easybuild-easyconfigs
Building wheels for collected packages: easybuild-easyconfigs
Building wheel for easybuild-easyconfigs (setup.py) ... [?25l- \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
[?25h Stored in directory: /home/travis/.cache/pip/wheels/60/83/5a/68a83b743a3b5a96bdb88de299d7630c9f272b0dec140d3e5d
Successfully built easybuild-easyconfigs
Installing collected packages: easybuild-easyconfigs
Successfully installed easybuild-easyconfigs-4.2.1.dev0
travis_time:end:052eda10:start=1588814055445647811,finish=1588814066257073859,duration=10811426048,event=script
[0K[32;1mThe command "cd $HOME; pip install $TRAVIS_BUILD_DIR" exited with 0.[0m
travis_time:start:29c5fb88
[0K$ export EB_PYTHON=python
travis_time:end:29c5fb88:start=1588814066260971025,finish=1588814066263322946,duration=2351921,event=script
[0K[32;1mThe command "export EB_PYTHON=python" exited with 0.[0m
travis_time:start:119f392e
[0K$ eb --show-config | tee eb_show_config.out
#
# Current EasyBuild configuration
# (C: command line argument, D: default value, E: environment variable, F: configuration file)
#
buildpath (D) = /home/travis/.local/easybuild/build
containerpath (D) = /home/travis/.local/easybuild/containers
installpath (D) = /home/travis/.local/easybuild
repositorypath (D) = /home/travis/.local/easybuild/ebfiles_repo
robot-paths (D) = /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs
sourcepath (D) = /home/travis/.local/easybuild/sources
travis_time:end:119f392e:start=1588814066266804980,finish=1588814066682593108,duration=415788128,event=script
[0K[32;1mThe command "eb --show-config | tee eb_show_config.out" exited with 0.[0m
travis_time:start:0136ac04
[0K$ grep "^robot-paths .*/easybuild/easyconfigs" eb_show_config.out
robot-paths (D) = /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs
travis_time:end:0136ac04:start=1588814066686554833,finish=1588814066690471317,duration=3916484,event=script
[0K[32;1mThe command "grep "^robot-paths .*/easybuild/easyconfigs" eb_show_config.out" exited with 0.[0m
travis_time:start:04bba5bb
[0K$ eb --search 'TensorFlow-1.14.*.eb' | tee eb_search_TF.out
* /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb
* /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-fosscuda-2019a-Python-3.7.2.eb
travis_time:end:04bba5bb:start=1588814066694135072,finish=1588814067330299771,duration=636164699,event=script
[0K[32;1mThe command "eb --search 'TensorFlow-1.14.*.eb' | tee eb_search_TF.out" exited with 0.[0m
travis_time:start:0266e428
[0K$ grep '/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb$' eb_search_TF.out
* /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb
travis_time:end:0266e428:start=1588814067334650224,finish=1588814067338587838,duration=3937614,event=script
[0K[32;1mThe command "grep '/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb$' eb_search_TF.out" exited with 0.[0m
travis_time:start:12fa85dc
[0K$ eb --search '^foss-2018b.eb' | tee eb_search_foss.out
* /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs/f/foss/foss-2018b.eb
travis_time:end:12fa85dc:start=1588814067342113207,finish=1588814067922486474,duration=580373267,event=script
[0K[32;1mThe command "eb --search '^foss-2018b.eb' | tee eb_search_foss.out" exited with 0.[0m
travis_time:start:11ac2748
[0K$ grep '/foss-2018b.eb$' eb_search_foss.out
* /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs/f/foss/foss-2018b.eb
travis_time:end:11ac2748:start=1588814067926556883,finish=1588814067930312710,duration=3755827,event=script
[0K[32;1mThe command "grep '/foss-2018b.eb$' eb_search_foss.out" exited with 0.[0m
travis_time:start:0cd3a8e0
[0K$ eb --prefix /tmp/$USER M4-1.4.18.eb
== temporary log file in case of crash /tmp/eb-j5yUKw/easybuild-ONrfqR.log
== processing EasyBuild easyconfig /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs/m/M4/M4-1.4.18.eb
== building and installing M4/1.4.18...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully (took 24 sec)
== Results of the build can be found in the log file(s) /tmp/travis/software/M4/1.4.18/easybuild/easybuild-M4-1.4.18-20200507.011453.log
== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-j5yUKw/easybuild-ONrfqR.log* have been removed.
== Temporary directory /tmp/eb-j5yUKw has been removed.
travis_time:end:0cd3a8e0:start=1588814067933671307,finish=1588814093254269867,duration=25320598560,event=script
[0K[32;1mThe command "eb --prefix /tmp/$USER M4-1.4.18.eb" exited with 0.[0m
Done. Your build exited with 1.
- 22161.2 - failed => https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/684076822
*bleep, bloop, I'm just a bot (boegelbot v20180813.01)*Please talk to my owner @boegel if you notice you me acting stupid),or submit a pull request to https://github.com/boegel/boegelbot fix the problem.
@jordiblasco: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/880684791 Output from first failing test suite run:
ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test/easyconfigs/easyconfigs.py", line 156, in test_conflicts
self.process_all_easyconfigs()
File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: picard/2.6.0-Java-11 (no easyconfig file or existing module found)'
======================================================================
ERROR: test_dep_graph (test.easyconfigs.easyconfigs.EasyConfigTest)
Unit test that builds a full dependency graph.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test/easyconfigs/easyconfigs.py", line 140, in test_dep_graph
self.process_all_easyconfigs()
File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: picard/2.6.0-Java-11 (no easyconfig file or existing module found)'
======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test/easyconfigs/easyconfigs.py", line 541, in test_dep_versions_per_toolchain_generation
self.process_all_easyconfigs()
File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: picard/2.6.0-Java-11 (no easyconfig file or existing module found)'
----------------------------------------------------------------------
Ran 12232 tests in 523.911s
FAILED (errors=3)
ERROR: Not all tests were successful.
bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice you me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.
closing as stale, can serve as a reference to add support for more recent versions of GenomeSTRiP
