{bio}[foss/2021a] BgeeDB v2.26.0 by SIB-software · Pull Request #18743 · easybuilders/easybuild-easyconfigs

SIB-software · 2023-09-08T08:17:08Z

(created using eb --new-pr)

verdurin · 2023-09-08T09:51:35Z

@boegelbot please test @ generoso

boegelbot · 2023-09-08T09:55:12Z

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

PR test command 'EB_PR=18743 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18743 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11669

Test results coming soon (I hope)...

Details

- notification for comment with ID 1711395461 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 · 2023-09-08T09:55:35Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 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/374ad15a87b2894aa3be9f3a7209a089 for a full test report.

verdurin · 2023-09-08T10:14:40Z

@SIB-software:
WARNING build failed (first 300 chars): Couldn't find file topGO_2.52.0.tar.gz anywhere, and downloading it didn't work either

smoretti · 2023-09-08T11:03:39Z

@verdurin the topGO tarball link looks fine.
Could you restart the bot?

branfosj · 2023-09-08T11:12:35Z

+        'https://bioconductor.org/packages/%(local_bioc_version)s/bioc/src/contrib/',
+        'https://bioconductor.org/packages/%(local_bioc_version)s/bioc/src/contrib/Archive/%(name)s',
+        'https://bioconductor.org/packages/%(local_bioc_version)s/data/annotation/src/contrib/',
+        'https://bioconductor.org/packages/%(local_bioc_version)s/data/experiment/src/contrib/',


Suggested change

'https://bioconductor.org/packages/%(local_bioc_version)s/bioc/src/contrib/',

'https://bioconductor.org/packages/%(local_bioc_version)s/bioc/src/contrib/Archive/%(name)s',

'https://bioconductor.org/packages/%(local_bioc_version)s/data/annotation/src/contrib/',

'https://bioconductor.org/packages/%(local_bioc_version)s/data/experiment/src/contrib/',

'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_bioc_version,

'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_bioc_version,

'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_bioc_version,

'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_bioc_version,

Local variables do not get replaced, so have to be used as per the suggested replacement instead.

So in the test report we see it trying to download with the %(local_bioc_version)s in the URL:

== 2023-09-08 09:55:32,644 filetools.py:832 WARNING URL https://bioconductor.org/packages/%(local_bioc_version)s/bioc/src/contrib/topGO_2.52.0.tar.gz was not found (HTTP response code 400), not trying again

branfosj · 2023-09-08T12:06:50Z

@boegelbot please test @ generoso

boegelbot · 2023-09-08T12:10:10Z

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

PR test command 'EB_PR=18743 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18743 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11674

Test results coming soon (I hope)...

Details

- notification for comment with ID 1711566745 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 · 2023-09-08T12:12:34Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/a85a78f9b6539afd6632f12a9ab14a7c for a full test report.

verdurin · 2023-09-08T15:35:49Z

@boegelbot please test @ jsc-zen2

verdurin · 2023-09-08T15:37:05Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/273f195f88a8a845d728f9dd748d84a8 for a full test report.

boegelbot · 2023-09-08T15:40:07Z

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

PR test command 'EB_PR=18743 EB_ARGS= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18743 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3335

Test results coming soon (I hope)...

Details

- notification for comment with ID 1711859107 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).

branfosj · 2023-09-09T11:39:02Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-09-09T11:40:08Z

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

PR test command 'EB_PR=18743 EB_ARGS= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18743 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3340

Test results coming soon (I hope)...

Details

- notification for comment with ID 1712490947 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 · 2023-09-09T11:41:52Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/278f3592088a12c1cd12799e7b160f15 for a full test report.

branfosj · 2023-09-09T11:42:45Z

Going in, thanks @SIB-software!

adding easyconfigs: BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb

81dceb5

verdurin added the new label Sep 8, 2023

branfosj reviewed Sep 8, 2023

View reviewed changes

Fix local variable replacement

832ee8a

branfosj approved these changes Sep 9, 2023

View reviewed changes

branfosj added this to the next release (4.8.1?) milestone Sep 9, 2023

branfosj merged commit 4e2674a into easybuilders:develop Sep 9, 2023

smoretti deleted the 20230908101658_new_pr_BgeeDB2260 branch September 11, 2023 07:18

Conversation

SIB-software commented Sep 8, 2023

Uh oh!

verdurin commented Sep 8, 2023

Uh oh!

boegelbot commented Sep 8, 2023

Uh oh!

boegelbot commented Sep 8, 2023

Uh oh!

verdurin commented Sep 8, 2023

Uh oh!

smoretti commented Sep 8, 2023

Uh oh!

branfosj Sep 8, 2023

Choose a reason for hiding this comment

Uh oh!

branfosj Sep 8, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

branfosj commented Sep 8, 2023

Uh oh!

boegelbot commented Sep 8, 2023

Uh oh!

boegelbot commented Sep 8, 2023

Uh oh!

verdurin commented Sep 8, 2023

Uh oh!

verdurin commented Sep 8, 2023

Uh oh!

boegelbot commented Sep 8, 2023

Uh oh!

branfosj commented Sep 9, 2023

Uh oh!

boegelbot commented Sep 9, 2023

Uh oh!

boegelbot commented Sep 9, 2023

Uh oh!

branfosj commented Sep 9, 2023

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

branfosj Sep 8, 2023 •

edited

Loading