{bio}[foss/2019a,intel/2019a] PheWAS v0.99.5-2

[murfreesboro]

(created using eb --new-pr)

[murfreesboro]

Test report by @murfreesboro
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
dev806.vampire - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.5
See https://gist.github.com/3f93934ce02c9d0f280190842317e0ac for a full test report.

[vanzod]

@murfreesboro The following libraries are already included in the R-3.6.0.*2019a installations with a matching version, hence they can be removed from the easyconfig files in your PR:

'crayon', '1.3.4'
'cli', '1.1.0'
'utf8', '1.1.4'
'tibble', '2.1.3'
'ggrepel', '0.8.1'
'R6', '2.4.0'
'crosstalk', '1.0.0'
'htmltools', '0.3.6'
'htmlwidgets', '1.3'

For those ones instead the version is different than the one installed with R.
Is there a specific compatibility reason for building them with a different version?

'Rcpp', '1.0.2'
'rlang', '0.4.0'
'pillar', '1.4.2'
'ggplot2', '3.2.1'
'DT', '0.8'

[murfreesboro]

OK I will take a look and modify.

[murfreesboro]

Test report by @murfreesboro
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
dev806.vampire - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.5
See https://gist.github.com/e2fdd8880934777461dbb222685db05d for a full test report.

[boegel]

@murfreesboro Ignore those failing tests, that obviously has nothing to do with your PR.

The tests got a bit stricter after collapsing the 4.x branch into develop, in preparation for the upcoming EasyBuild v4.0.0 release, in particular w.r.t. the 'dummy toolchain (should now be system), and the naming of local variables in easyconfig files (see https://easybuild.readthedocs.io/en/4.x/Easyconfig-files-local-variables.html).

A couple of easyconfigs in develop were not fixed yet to pass these tests, those were fixed in #8822, so I've re-triggered the tests for this PR.

[boegelbot]

Travis test report: 5/5 runs failed - see https://travis-ci.org/easybuilders/easybuild-easyconfigs/builds/576016268

Only showing partial log for 1st failed test suite run 16536.1;
full log at https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/576016269

...
ERROR: Test for parsing of easyconfig PheWAS-0.99.5-2-foss-2019a-R-3.6.0.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "<string>", line 1, in innertest
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 523, in template_easyconfig_test
    ecs = process_easyconfig(spec)
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-4.0.0.dev0-py2.6.egg/easybuild/framework/easyconfig/easyconfig.py", line 1764, in process_easyconfig
    raise EasyBuildError("Failed to process easyconfig %s: %s", spec, err.msg)
EasyBuildError: "Failed to process easyconfig /home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/p/PheWAS/PheWAS-0.99.5-2-foss-2019a-R-3.6.0.eb: Use of 1 unknown easyconfig parameters detected in PheWAS-0.99.5-2-foss-2019a-R-3.6.0.eb: commit\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically."

======================================================================
ERROR: Test for parsing of easyconfig PheWAS-0.99.5-2-intel-2019a-R-3.6.0.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "<string>", line 1, in innertest
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 523, in template_easyconfig_test
    ecs = process_easyconfig(spec)
  File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/easybuild_framework-4.0.0.dev0-py2.6.egg/easybuild/framework/easyconfig/easyconfig.py", line 1764, in process_easyconfig
    raise EasyBuildError("Failed to process easyconfig %s: %s", spec, err.msg)
EasyBuildError: "Failed to process easyconfig /home/travis/build/easybuilders/easybuild-easyconfigs/easybuild/easyconfigs/p/PheWAS/PheWAS-0.99.5-2-intel-2019a-R-3.6.0.eb: Use of 1 unknown easyconfig parameters detected in PheWAS-0.99.5-2-intel-2019a-R-3.6.0.eb: commit\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically."

======================================================================
FAIL: 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 502, in test_changed_files_pull_request
    self.assertTrue(False, error_msg)
AssertionError: Failed to find parsed easyconfig for PheWAS-0.99.5-2-foss-2019a-R-3.6.0.eb (and could not isolate it in easyconfigs archive either)

----------------------------------------------------------------------
Ran 8259 tests in 413.546s

FAILED (failures=1, errors=2)
ERROR: Not all tests were successful.

• 16536.2 - errored => https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/576016270
• 16536.3 - errored => https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/576016271
• 16536.4 - errored => https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/576016272
• 16536.5 - errored => https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/576016273

*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.

[murfreesboro]

Test report by @murfreesboro
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
dev806.vampire - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.5
See https://gist.github.com/97f6be998938ef14d0a8e4315f42d1d0 for a full test report.

[vanzod]

Test report by @vanzod
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
cermis - Linux debian 9.9, Intel(R) Xeon(R) CPU X5670 @ 2.93GHz, Python 2.7.13
See https://gist.github.com/1fc306eb7e4f64bf690cb1dd03993ad1 for a full test report.

[vanzod]

Going in, thanks @murfreesboro!