add missMDA extension to R-bundle-CRAN 2023.12 by pavelToman · Pull Request #21167 · easybuilders/easybuild-easyconfigs

pavelToman · 2024-08-12T12:53:25Z

resolves vscentrum/vsc-software-stack#374

pavelToman · 2024-08-12T12:53:47Z

@boegelbot please test @ generoso

boegelbot · 2024-08-12T12:55:09Z

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

PR test command 'EB_PR=21167 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21167 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14050

Test results coming soon (I hope)...

Details

- notification for comment with ID 2283907638 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 · 2024-08-13T10:29:56Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--skip"

boegelbot · 2024-08-13T10:30:19Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21167 EB_ARGS="--skip" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21167 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4664

Test results coming soon (I hope)...

Details

- notification for comment with ID 2285915516 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 · 2024-08-13T10:45:28Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/56d64fa6b261c414dbbaa451b363a7da for a full test report.

boegel · 2024-08-13T11:32:39Z

More info on failing sanity check for renv (which, at first sight, has nothing to do with the changes being made here, but maybe there's a side effect of some sort):

== 2024-08-13 11:06:53,549 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Sanity check failed: extensions sanity check failed for 1 extensions: renv
failing sanity check for 'renv' extension: command "R -q --no-save" (stdin: "pkgver = packageVersion('renv'); if (pkgver != '1.0.3')  { stop('renv 1.0.3 not installed, found ', pkgver, ' instead') }") failed; output:
> pkgver = packageVersion('renv'); if (pkgver != '1.0.3')  { stop('renv 1.0.3 not installed, found ', pkgver, ' instead') }
Error: renv 1.0.3 not installed, found 1.0.7.9000 instead

branfosj · 2024-08-13T11:43:26Z

renv 1.07.900 is the latest development version - so not a released version?!

boegel · 2024-08-13T15:30:50Z

Somehow it got installed in the home directory of the bot:

[boegelbot@jsczen3l1 ~]$ grep Version /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/renv/DESCRIPTION
Version: 1.0.7.9000

It looks like this was triggered somehow on 31 July 2024 (so I know it wasn't me):

[boegelbot@jsczen3l1 ~]$ ls -ld /home/boegelbot/R/x86_64-pc-linux-gnu-library/*/*
drwxr-xr-x. 11 boegelbot boegelbot  179 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/digest
drwxr-xr-x.  8 boegelbot boegelbot  153 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/purrr
drwxr-xr-x. 12 boegelbot boegelbot 4096 May 27 21:42 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/renv
drwxr-xr-x. 10 boegelbot boegelbot 4096 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown
drwxr-xr-x. 11 boegelbot boegelbot 4096 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/testthat
drwxr-xr-x. 10 boegelbot boegelbot  183 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/xml2
drwxr-xr-x.  8 boegelbot boegelbot  190 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/yaml

I've removed all of these, and did a chmod 000 on /home/boegelbot/R/x86_64-pc-linux-gnu-library.

edit: very similar situation also on generoso, also cleaned it up:

[boegelbot@login1 ~]$ ls -lrtd R/x86_64-pc-linux-gnu-library/*/*
drwxrwxr-x. 12 boegelbot boegelbot 4.0K May 27 16:23 R/x86_64-pc-linux-gnu-library/4.3/renv
drwxrwxr-x. 11 boegelbot boegelbot 4.0K Jul 29 14:18 R/x86_64-pc-linux-gnu-library/4.3/digest
drwxrwxr-x.  8 boegelbot boegelbot 4.0K Jul 29 14:18 R/x86_64-pc-linux-gnu-library/4.3/purrr
drwxrwxr-x.  8 boegelbot boegelbot 4.0K Jul 29 14:18 R/x86_64-pc-linux-gnu-library/4.3/yaml
drwxrwxr-x. 10 boegelbot boegelbot 4.0K Jul 29 14:18 R/x86_64-pc-linux-gnu-library/4.3/rmarkdown
drwxrwxr-x. 11 boegelbot boegelbot 4.0K Jul 29 14:19 R/x86_64-pc-linux-gnu-library/4.3/testthat
drwxrwxr-x. 10 boegelbot boegelbot 4.0K Jul 29 14:19 R/x86_64-pc-linux-gnu-library/4.3/xml2
[boegelbot@login1 ~]$ grep Version R/x86_64-pc-linux-gnu-library/4.3/renv/DESCRIPTION
Version: 1.0.7.9000

boegel · 2024-08-13T15:31:12Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--skip"

boegelbot · 2024-08-13T15:40:11Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21167 EB_ARGS="--skip" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21167 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4671

Test results coming soon (I hope)...

Details

- notification for comment with ID 2286540971 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 · 2024-08-13T15:58:55Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/ec16c6006d49b473c838805056f98a3b for a full test report.

boegel · 2024-08-13T16:04:13Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3103.skitty.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/boegel/94847818104502c23fa564151da8bc4e for a full test report.

branfosj · 2024-08-13T16:12:34Z

Somehow it got installed in the home directory of the bot:

[boegelbot@jsczen3l1 ~]$ grep Version /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/renv/DESCRIPTION
Version: 1.0.7.9000

It looks like this was triggered somehow on 31 July 2024 (so I know it wasn't me):

[boegelbot@jsczen3l1 ~]$ ls -ld /home/boegelbot/R/x86_64-pc-linux-gnu-library/*/*
drwxr-xr-x. 11 boegelbot boegelbot  179 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/digest
drwxr-xr-x.  8 boegelbot boegelbot  153 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/purrr
drwxr-xr-x. 12 boegelbot boegelbot 4096 May 27 21:42 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/renv
drwxr-xr-x. 10 boegelbot boegelbot 4096 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown
drwxr-xr-x. 11 boegelbot boegelbot 4096 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/testthat
drwxr-xr-x. 10 boegelbot boegelbot  183 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/xml2
drwxr-xr-x.  8 boegelbot boegelbot  190 Jul 31 11:11 /home/boegelbot/R/x86_64-pc-linux-gnu-library/4.3/yaml

I've removed all of these, and did a chmod 000 on /home/boegelbot/R/x86_64-pc-linux-gnu-library.

edit: very similar situation also on generoso, also cleaned it up:

[boegelbot@login1 ~]$ ls -lrtd R/x86_64-pc-linux-gnu-library/*/*
drwxrwxr-x. 12 boegelbot boegelbot 4.0K May 27 16:23 R/x86_64-pc-linux-gnu-library/4.3/renv
drwxrwxr-x. 11 boegelbot boegelbot 4.0K Jul 29 14:18 R/x86_64-pc-linux-gnu-library/4.3/digest
drwxrwxr-x.  8 boegelbot boegelbot 4.0K Jul 29 14:18 R/x86_64-pc-linux-gnu-library/4.3/purrr
drwxrwxr-x.  8 boegelbot boegelbot 4.0K Jul 29 14:18 R/x86_64-pc-linux-gnu-library/4.3/yaml
drwxrwxr-x. 10 boegelbot boegelbot 4.0K Jul 29 14:18 R/x86_64-pc-linux-gnu-library/4.3/rmarkdown
drwxrwxr-x. 11 boegelbot boegelbot 4.0K Jul 29 14:19 R/x86_64-pc-linux-gnu-library/4.3/testthat
drwxrwxr-x. 10 boegelbot boegelbot 4.0K Jul 29 14:19 R/x86_64-pc-linux-gnu-library/4.3/xml2
[boegelbot@login1 ~]$ grep Version R/x86_64-pc-linux-gnu-library/4.3/renv/DESCRIPTION
Version: 1.0.7.9000

RStudio-Server installs. Specifically #21086 and #20060

In those we have ./install-packages and the packages installed are:

  digest
  purrr
  rmarkdown
  testthat
  xml2
  yaml

and further down that we see renv being installed.

boegel · 2024-08-13T21:26:06Z

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

boegelbot · 2024-08-13T21:30:05Z

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

PR test command 'EB_PR=21167 EB_ARGS="--skip" EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21167 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14065

Test results coming soon (I hope)...

Details

- notification for comment with ID 2287165758 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 · 2024-08-13T21:51:51Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns2 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/e55ff2d737c1d3a4e0e941fd5c3f8797 for a full test report.

boegel

lgtm

boegel · 2024-08-14T11:14:22Z

Going in, thanks @pavelToman!

Update R-bundle-CRAN-2023.12-foss-2023a.eb add missMDA

2e1fe4f

pavelToman mentioned this pull request Aug 12, 2024

missMDA vscentrum/vsc-software-stack#374

Closed

2 tasks

boegel changed the title ~~Update R-bundle-CRAN-2023.12-foss-2023a.eb - add missMDA 1.19~~ add missMDA extension to R-bundle-CRAN 2023.12 Aug 13, 2024

boegel added the enhancement label Aug 13, 2024

boegel added this to the 4.x milestone Aug 13, 2024

branfosj mentioned this pull request Aug 13, 2024

stop RStudio-Server 2023.09 from installing R packages (+ move to foss/2023a toolchain) #21175

Merged

boegel modified the milestones: 4.x, release after 4.9.2 Aug 14, 2024

boegel approved these changes Aug 14, 2024

View reviewed changes

boegel merged commit 46baccd into easybuilders:develop Aug 14, 2024

boegel mentioned this pull request Aug 14, 2024

add missMDA extension to R-bundle-CRAN 2024.06 #21183

Merged

Conversation

pavelToman commented Aug 12, 2024

Uh oh!

pavelToman commented Aug 12, 2024

Uh oh!

boegelbot commented Aug 12, 2024

Uh oh!

boegel commented Aug 13, 2024

Uh oh!

boegelbot commented Aug 13, 2024

Uh oh!

boegelbot commented Aug 13, 2024

Uh oh!

boegel commented Aug 13, 2024

Uh oh!

branfosj commented Aug 13, 2024

Uh oh!

boegel commented Aug 13, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

boegel commented Aug 13, 2024

Uh oh!

boegelbot commented Aug 13, 2024

Uh oh!

boegelbot commented Aug 13, 2024

Uh oh!

boegel commented Aug 13, 2024

Uh oh!

branfosj commented Aug 13, 2024

Uh oh!

boegel commented Aug 13, 2024

Uh oh!

boegelbot commented Aug 13, 2024

Uh oh!

boegelbot commented Aug 13, 2024

Uh oh!

boegel left a comment

Choose a reason for hiding this comment

Uh oh!

boegel commented Aug 14, 2024

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

boegel commented Aug 13, 2024 •

edited

Loading