{bio}[foss/2019b] GRIDSS-2.9.3-foss-2019b-Java-11.eb and dependencies

[jordiblasco]

(created using eb --new-pr)

[boegelbot]

Travis test report: 2/2 runs failed - see https://travis-ci.org/easybuilders/easybuild-easyconfigs/builds/706380934

Only showing partial log for 1st failed test suite run 23179.1; full log at https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/706380935

...
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 774, in test_changed_files_pull_request
    self.check_https(changed_ecs)
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 699, in check_https
    self.assertFalse(failing_checks, '\n'.join(failing_checks))
AssertionError: Found http:// URL in picard-2.6.0-Java-11.eb, should be https:// : http://sourceforge.net/projects/picard

======================================================================
FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 486, in test_dep_versions_per_toolchain_generation
    self.assertFalse(multi_dep_vars, error_msg)
AssertionError: No multi-variant deps found for '^.*-(?P<tc_gen>201[89][ab]).*\.eb$' easyconfigs:

found 2 variants of 'picard' dependency in easyconfigs using '2019b' toolchain generation
* version: 2.21.6; versionsuffix: -Java-11 as dep for set(['FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb', 'SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb'])
* version: 2.6.0; versionsuffix:  as dep for set(['GRIDSS-2.9.3-foss-2019b-Java-11.eb'])


----------------------------------------------------------------------
Ran 10162 tests in 623.635s

FAILED (failures=3)
ERROR: Not all tests were successful.
travis_time:end:30c9b450:start=1594261488126882054,finish=1594262113827167780,duration=625700285726,event=script
[0K[31;1mThe command "python -O -m test.easyconfigs.suite" exited with 2.[0m
travis_time:start:086334c6
[0K$ unset PYTHONPATH
travis_time:end:086334c6:start=1594262113831179090,finish=1594262113833628255,duration=2449165,event=script
[0K[32;1mThe command "unset PYTHONPATH" exited with 0.[0m
travis_time:start:1332f5f0
[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-4.2.3.dev0
travis_time:end:1332f5f0:start=1594262113837281062,finish=1594262124871449944,duration=11034168882,event=script
[0K[32;1mThe command "cd $HOME; pip install $TRAVIS_BUILD_DIR" exited with 0.[0m
travis_time:start:0042e01e
[0K$ export EB_PYTHON=python
travis_time:end:0042e01e:start=1594262124875257032,finish=1594262124877571339,duration=2314307,event=script
[0K[32;1mThe command "export EB_PYTHON=python" exited with 0.[0m
travis_time:start:2030fcc7
[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:2030fcc7:start=1594262124881040388,finish=1594262125289665896,duration=408625508,event=script
[0K[32;1mThe command "eb --show-config | tee eb_show_config.out" exited with 0.[0m
travis_time:start:15295898
[0K$ grep "^robot-paths .*/easybuild/easyconfigs" eb_show_config.out
robot-paths    (D) = /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs
travis_time:end:15295898:start=1594262125293898482,finish=1594262125297804693,duration=3906211,event=script
[0K[32;1mThe command "grep "^robot-paths .*/easybuild/easyconfigs" eb_show_config.out" exited with 0.[0m
travis_time:start:007400e5
[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:007400e5:start=1594262125301410374,finish=1594262125885740736,duration=584330362,event=script
[0K[32;1mThe command "eb --search 'TensorFlow-1.14.*.eb' | tee eb_search_TF.out" exited with 0.[0m
travis_time:start:0da01295
[0K$ grep '/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb$' eb_search_TF.out
 * /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb
travis_time:end:0da01295:start=1594262125889778764,finish=1594262125893502183,duration=3723419,event=script
[0K[32;1mThe command "grep '/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb$' eb_search_TF.out" exited with 0.[0m
travis_time:start:08113db8
[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:08113db8:start=1594262125896723032,finish=1594262126470495447,duration=573772415,event=script
[0K[32;1mThe command "eb --search '^foss-2018b.eb' | tee eb_search_foss.out" exited with 0.[0m
travis_time:start:11224282
[0K$ grep '/foss-2018b.eb$' eb_search_foss.out
 * /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs/f/foss/foss-2018b.eb
travis_time:end:11224282:start=1594262126474528588,finish=1594262126478077538,duration=3548950,event=script
[0K[32;1mThe command "grep '/foss-2018b.eb$' eb_search_foss.out" exited with 0.[0m
travis_time:start:1fdefc32
[0K$ eb --prefix /tmp/$USER M4-1.4.18.eb
== temporary log file in case of crash /tmp/eb-ov_t3s/easybuild-n7W583.log
== processing EasyBuild easyconfig /home/travis/virtualenv/python2.7.15/easybuild/easyconfigs/m/M4/M4-1.4.18.eb
== building and installing M4/1.4.18...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully (took 24 sec)
== Results of the build can be found in the log file(s) /tmp/travis/software/M4/1.4.18/easybuild/easybuild-M4-1.4.18-20200709.023551.log
== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-ov_t3s/easybuild-n7W583.log* have been removed.
== Temporary directory /tmp/eb-ov_t3s has been removed.
travis_time:end:1fdefc32:start=1594262126481346746,finish=1594262151117830984,duration=24636484238,event=script
[0K[32;1mThe command "eb --prefix /tmp/$USER M4-1.4.18.eb" exited with 0.[0m


Done. Your build exited with 1.

• 23179.2 - failed => https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/706380936

*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.

[boegelbot]

@jordiblasco: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/880672521 Output from first failing test suite run:

FAIL: test__parse_easyconfig_picard-2.6.0-Java-11.eb (test.easyconfigs.easyconfigs.EasyConfigTest)
Test for easyconfig picard-2.6.0-Java-11.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 1255, in innertest
    template_easyconfig_test(self, spec_path)
  File "test/easyconfigs/easyconfigs.py", line 1084, 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 "test/easyconfigs/easyconfigs.py", line 994, in test_changed_files_pull_request
    self.check_https(changed_ecs)
  File "test/easyconfigs/easyconfigs.py", line 904, in check_https
    self.fail('\n'.join(failing_checks))
AssertionError: Found http:// URL in picard-2.6.0-Java-11.eb, should be https:// : http://sourceforge.net/projects/picard

======================================================================
FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 607, in test_dep_versions_per_toolchain_generation
    self.assertFalse(multi_dep_vars, error_msg)
AssertionError: No multi-variant deps found for '^.*-(?P<tc_gen>201[89][ab]).*\.eb$' easyconfigs:

found 2 variants of 'picard' dependency in easyconfigs using '2019b' toolchain generation
* version: 2.21.6; versionsuffix: -Java-11 as dep for set(['FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb', 'SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb', 'FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb'])
* version: 2.6.0; versionsuffix:  as dep for set(['GRIDSS-2.9.3-foss-2019b-Java-11.eb'])


----------------------------------------------------------------------
Ran 12231 tests in 365.075s

FAILED (failures=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.

[akesandgren]

Toolchain is a bit old and it's superceeded by #18170