{bio}[foss/2022b] leafcutter v0.2.9 w/ R 4.2.2 + additional required extensions in R-bundle-Bioconductor v3.16 by laraPPr · Pull Request #18615 · easybuilders/easybuild-easyconfigs

laraPPr · 2023-08-22T11:38:35Z

(created using eb --new-pr)

requires:

{bio}[foss/2022b] RegTools v1.0.0 #18568

…r with depencies for leafcutterMD

boegel · 2023-08-22T13:40:45Z

@boegelbot please test @ generoso
EB_ARGS="--skip"

boegelbot · 2023-08-22T13:45:12Z

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

PR test command 'EB_PR=18615 EB_ARGS="--skip" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18615 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11527

Test results coming soon (I hope)...

Details

- notification for comment with ID 1688212582 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 · 2023-08-22T13:58:39Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns2 - 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/ed6ecb76ca41daa32aba0e4de594263c for a full test report.

boegel · 2023-08-22T14:03:32Z

@boegelbot please test @ jsc-zen2
EB_ARGS="--skip"

boegelbot · 2023-08-22T14:07:09Z

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

PR test command 'EB_PR=18615 EB_ARGS="--skip" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18615 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3223

Test results coming soon (I hope)...

Details

- notification for comment with ID 1688252530 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).

boegel · 2023-08-22T14:08:51Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (2 easyconfigs in total)
node3104.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/374ea761be8ea68144e6b0dba5320e11 for a full test report.

boegel · 2023-08-22T17:12:10Z

@boegelbot please test @ jsc-zen2
EB_ARGS="--sanity-check-only"

boegelbot · 2023-08-22T17:27:09Z

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

PR test command 'EB_PR=18615 EB_ARGS="--sanity-check-only" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18615 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3225

Test results coming soon (I hope)...

Details

- notification for comment with ID 1688604091 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 · 2023-08-22T17:30:22Z

Test report by @boegelbot
FAILED
Build succeeded for 1 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/7b732d1bcc6a524c1a2393bb0c6b128e for a full test report.

boegel · 2023-08-23T15:27:24Z

--sanity-check-only failed with "/bin/bash: R: command not found" because of a bug in RPackage easyblock, which makes it incompatible with --sanity-check-only, similar to what we had for PythonPackage before easybuilders/easybuild-easyblocks#2828 was fixed...

edit: issue opened at easybuilders/easybuild-easyblocks#2986

boegel · 2023-08-23T15:27:37Z

@boegelbot please test @ jsc-zen2
EB_ARGS="--skip"

boegelbot · 2023-08-23T15:32:09Z

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

PR test command 'EB_PR=18615 EB_ARGS="--skip" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18615 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3227

Test results coming soon (I hope)...

Details

- notification for comment with ID 1690171359 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 · 2023-08-23T15:40:33Z

Test report by @boegelbot
FAILED
Build succeeded for 1 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/443f73fbb003173a5d5fe9fcc34bfc0a for a full test report.

boegel · 2023-08-24T09:38:16Z

@boegelbot please test @ jsc-zen2
EB_ARGS="leafcutter-0.2.9-foss-2022b-R-4.2.2.eb"

boegelbot · 2023-08-24T09:42:08Z

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

PR test command 'EB_PR=18615 EB_ARGS="leafcutter-0.2.9-foss-2022b-R-4.2.2.eb" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18615 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3234

Test results coming soon (I hope)...

Details

- notification for comment with ID 1691351735 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 · 2023-08-24T09:47:27Z

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/1db2aed2caecdcd50e0402c040e8d046 for a full test report.

boegel · 2023-08-24T10:31:35Z

Going in, thanks @laraPPr!

vsc46128 and others added 3 commits August 22, 2023 13:38

new easyconfig for leafcutterMD and an update of R-bundle-Bioconducto…

eeac8d5

…r with depencies for leafcutterMD

cleanup style

bf93860

update R-bundle-Bioconductor

1794984

boegel requested changes Aug 22, 2023

View reviewed changes

Comment thread easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

boegel added enhancement new labels Aug 22, 2023

boegel added this to the 4.x milestone Aug 22, 2023

update style leafcutter.eb

9e4cea1

easybuilders deleted a comment from boegelbot Aug 22, 2023

add missing extentions

a1f13f8

boegel changed the title ~~new easyconfig for leafcutterMD and an update of R-bundle-Bioconductor with depencies for leafcutterMD~~ {bio}[foss/2022b] leafcutter v0.2.9 w/ R 4.2.2 + additional required extensions in R-bundle-Bioconductor v.316 Aug 22, 2023

boegel changed the title ~~{bio}[foss/2022b] leafcutter v0.2.9 w/ R 4.2.2 + additional required extensions in R-bundle-Bioconductor v.316~~ {bio}[foss/2022b] leafcutter v0.2.9 w/ R 4.2.2 + additional required extensions in R-bundle-Bioconductor v3.16 Aug 22, 2023

boegel approved these changes Aug 24, 2023

View reviewed changes

boegel merged commit 8267e90 into easybuilders:develop Aug 24, 2023

boegel modified the milestones: 4.x, next release (4.8.1?) Aug 24, 2023

This was referenced Aug 25, 2023

LeafCutter vscentrum/vsc-software-stack#162

Closed

Leafcutter vscentrum/vsc-software-stack#187

Closed

Conversation

laraPPr commented Aug 22, 2023 • edited by boegel Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

boegel commented Aug 22, 2023

Uh oh!

boegelbot commented Aug 22, 2023

Uh oh!

boegelbot commented Aug 22, 2023

Uh oh!

boegel commented Aug 22, 2023

Uh oh!

boegelbot commented Aug 22, 2023

Uh oh!

boegel commented Aug 22, 2023

Uh oh!

boegel commented Aug 22, 2023

Uh oh!

boegelbot commented Aug 22, 2023

Uh oh!

boegelbot commented Aug 22, 2023

Uh oh!

boegel commented Aug 23, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

boegel commented Aug 23, 2023

Uh oh!

boegelbot commented Aug 23, 2023

Uh oh!

boegelbot commented Aug 23, 2023

Uh oh!

boegel commented Aug 24, 2023

Uh oh!

boegelbot commented Aug 24, 2023

Uh oh!

boegelbot commented Aug 24, 2023

Uh oh!

boegel commented Aug 24, 2023

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

laraPPr commented Aug 22, 2023 •

edited by boegel

Loading

boegel commented Aug 23, 2023 •

edited

Loading