{bio,tools}[foss/2022a] ResistanceGA v4.2-5, RCall v0.13.17 w/ R 4.2.1 Julia 1.9.2 #18933

ItIsI-Orient · 2023-10-06T10:55:43Z

(created using eb --new-pr)

….eb, RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb and patches: JuliaCall-0.17.5-top_level_macro.patch

ItIsI-Orient · 2023-10-06T12:29:28Z

@boegelbot please test @ generoso

boegelbot · 2023-10-06T12:30:11Z

@ItIsI-Orient: Request for testing this PR well received on login1

PR test command 'EB_PR=18933 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_18933 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11871

Test results coming soon (I hope)...

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boegelbot · 2023-10-06T12:44:40Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/b29d48e1edf65670f423c93ee5fa21a9 for a full test report.

ItIsI-Orient · 2023-10-06T13:58:16Z

@boegelbot please test @ generoso

boegelbot · 2023-10-06T14:00:05Z

@ItIsI-Orient: Request for testing this PR well received on login1

PR test command 'EB_PR=18933 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_18933 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11872

Test results coming soon (I hope)...

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boegelbot · 2023-10-06T14:09:40Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/77aa4983bf11d2811303062af71a7567 for a full test report.

ItIsI-Orient · 2023-10-06T14:48:05Z

@boegelbot please test @ generoso

boegelbot · 2023-10-06T14:50:10Z

@ItIsI-Orient: Request for testing this PR well received on login1

PR test command 'EB_PR=18933 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_18933 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11873

Test results coming soon (I hope)...

- notification for comment with ID 1750808918 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-10-06T15:01:41Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/1cfebfaf419fc571a7f0fa25b7058543 for a full test report.

boegelbot · 2023-10-09T16:25:48Z

@ItIsI-Orient: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/6458688453
Output from first failing test suite run:

FAIL: test__parse_easyconfig_ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb (test.easyconfigs.easyconfigs.EasyConfigTest)
Test for easyconfig ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1609, in innertest
    template_easyconfig_test(self, spec_path)
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1510, in template_easyconfig_test
    self.fail("Verification of patches for %s failed:\n%s" % (ec_fn, '\n'.join(ext_patch_issues)))
AssertionError: Verification of patches for ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb failed:
Invalid checksum for patch JuliaCall-0.17.5-top_level_macro.patch for extension ResistanceGA: {'JuliaCall-0.17.5-top_level_macro.patch': 'a733768f4bddd391a74d588b3d47bf8cbd475b42147856b35b0efd2eff83f63a'}.

----------------------------------------------------------------------
Ran 18228 tests in 864.302s

FAILED (failures=1)
ERROR: Not all tests were successful

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ItIsI-Orient · 2023-10-09T21:56:32Z

@boegelbot please test @ generoso

boegelbot · 2023-10-09T22:00:04Z

@ItIsI-Orient: Request for testing this PR well received on login1

PR test command 'EB_PR=18933 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_18933 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11907

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-10-09T22:14:31Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/0d1ddf6d2587070dcdb716461eab1c8b for a full test report.

ItIsI-Orient · 2023-10-10T02:04:36Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-10-10T02:05:08Z

@ItIsI-Orient: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18933 EB_ARGS= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18933 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3524

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-10-10T02:14:14Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 2 (2 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/945f36a122522f8a7d28948ed34ea8c4 for a full test report.

smoors · 2023-10-10T09:58:40Z

below is the error in jsc-zen2, maybe add a patch to disable the graphics test here https://github.com/JuliaInterop/RCall.jl/blob/01e006271142c62554ccabc1194680fc7f4156a3/test/basic.jl#L98

basic
ERROR: LoadError: REvalError: Warning in png("/tmp/eb-pj6wd1kw/jl_xw3odOra1G") :
unable to open connection to X11 display ''
Error in .External2(C_X11, paste0("png::", filename), g$width, g$height, :
unable to start device PNG
Calls: png
in expression starting at /project/def-maintainers/boegelbot/Rocky8/zen2/software/RCall/0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2/packages/RCall/test/basic.jl:100
in expression starting at /project/def-maintainers/boegelbot/Rocky8/zen2/software/RCall/0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2/packages/RCall/test/runtests.jl:60
ERROR: Package RCall errored during testing

smoors · 2023-10-11T18:55:37Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-10-11T19:05:11Z

@smoors: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18933 EB_ARGS= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18933 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3532

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch

boegelbot · 2023-10-11T19:16:07Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/255e7156f1964e8885f8b4a54a848ccd for a full test report.

smoors · 2023-10-12T15:48:23Z

@boegelbot: please test @ generoso

boegelbot · 2023-10-12T15:50:05Z

@smoors: Request for testing this PR well received on login1

PR test command 'EB_PR=18933 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_18933 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11926

Test results coming soon (I hope)...

- notification for comment with ID 1759887500 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-10-12T16:04:26Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/0b623fb3b7866145862c9586bdd2e92b for a full test report.

smoors

lgtm

smoors · 2023-10-12T16:13:08Z

Going in, thanks @ItIsI-Orient!

adding easyconfigs: ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2…

9e9bd63

….eb, RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb and patches: JuliaCall-0.17.5-top_level_macro.patch

ItIsI-Orient added the new label Oct 6, 2023

ItIsI-Orient mentioned this pull request Oct 6, 2023

ResistanceGA vscentrum/vsc-software-stack#29

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Fixed sources being str

50c04c2

branfosj added this to the 4.x milestone Oct 6, 2023

Fixed line endings in patch

21b2c3a

Fixed l checksum for the patch

3aa7707

Removed comment from the top of the patch, since it caused problems

a7d5b47

Changed checksum for the patch

1cad3ae

Added patch to disable test on gpu

b663a4c

smoors reviewed Oct 11, 2023

View reviewed changes

easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch Show resolved Hide resolved

Orient added 2 commits October 12, 2023 14:16

Added patch description

3b95c24

Update RCall

ebebd3b

smoors modified the milestones: 4.x, next release (4.8.2?) Oct 12, 2023

smoors approved these changes Oct 12, 2023

View reviewed changes

smoors merged commit 8118716 into easybuilders:develop Oct 12, 2023
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{bio,tools}[foss/2022a] ResistanceGA v4.2-5, RCall v0.13.17 w/ R 4.2.1 Julia 1.9.2 #18933

{bio,tools}[foss/2022a] ResistanceGA v4.2-5, RCall v0.13.17 w/ R 4.2.1 Julia 1.9.2 #18933

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{bio,tools}[foss/2022a] ResistanceGA v4.2-5, RCall v0.13.17 w/ R 4.2.1 Julia 1.9.2 #18933

{bio,tools}[foss/2022a] ResistanceGA v4.2-5, RCall v0.13.17 w/ R 4.2.1 Julia 1.9.2 #18933

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