add additional extensions to to R-bundle-CRAN 2025.11 by pavelToman · Pull Request #25181 · easybuilders/easybuild-easyconfigs

pavelToman · 2026-01-29T14:28:08Z

Updated to add same packages as in #25179

pavelToman · 2026-01-29T14:29:58Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-01-29T14:40:08Z

@pavelToman: 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=25181 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25181 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9529

Test results coming soon (I hope)...

Details

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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 · 2026-01-30T07:35:19Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 16 hours 54 mins 52 secs) (1 easyconfigs in total)
jsczen3c3.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/d7df68d7141a8b2acdbeeb5381bc2109 for a full test report.

pavelToman · 2026-01-31T04:39:17Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (total: 17 hours 45 mins 29 secs) (1 easyconfigs in total)
node4012.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/8cc9143831de534bdfb420df3f19c4fe for a full test report.

pavelToman · 2026-02-02T13:01:45Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-02-02T13:10:13Z

@pavelToman: 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=25181 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25181 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9542

Test results coming soon (I hope)...

Details

- notification for comment with ID 3834988053 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).

Thyre · 2026-02-02T13:57:52Z

@pavelToman It's a very good idea to pass

CORE_CNT=16
EB_ARGS="--parallel-extensions-install"

to jsc-zen3 for these bundles, especially with the amount of extensions in R-bundle-CRAN (and other R bundles).
Tests will take significantly longer otherwise (at least 2x).

boegelbot · 2026-02-03T07:23:46Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 18 hours 13 mins 12 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/df5508a2266b4f695d6807ce215e8d22 for a full test report.

pavelToman · 2026-02-03T08:50:59Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16
EB_ARGS="--parallel-extensions-install"

boegelbot · 2026-02-03T09:00:11Z

@pavelToman: 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=25181 EB_ARGS="--parallel-extensions-install" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25181 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9552

Test results coming soon (I hope)...

Details

- notification for comment with ID 3839953096 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 · 2026-02-03T19:23:36Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 10 hours 20 mins 35 secs) (1 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/e38a1164f86122f882e801f9e98fee45 for a full test report.

pavelToman · 2026-02-05T12:36:24Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (total: 16 hours 57 mins 36 secs) (1 easyconfigs in total)
node4202.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/55c9e805959e93a4f350c2dba75452e8 for a full test report.

Thyre · 2026-02-10T12:21:13Z

Test report by @Thyre
SUCCESS
Build succeeded for 1 out of 1 (total: 3 hours 21 mins 0 secs) (1 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.7, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 590.48.01, Python 3.9.25
See https://gist.github.com/Thyre/c8a9881dc695de4e4b0ef8401fa84f8a for a full test report.

laraPPr

lgtm

boegel

lgtm

boegel · 2026-02-11T16:02:27Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (total: 41 mins 6 secs) (1 easyconfigs in total)
node4204.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/boegel/1c046fd5ddb8d76e8f8c302e7af0ee1b for a full test report.

laraPPr · 2026-02-11T17:25:39Z

Test report by @laraPPr
SUCCESS
Build succeeded for 1 out of 1 (total: 6 hours 51 mins 52 secs) (1 easyconfigs in total)
node3589.doduo.os - Linux RHEL 9.6 (Plow), x86_64, AMD EPYC 7552 48-Core Processor, Python 3.9.21
See https://gist.github.com/laraPPr/0f06811bef8c531325f134e6ec657da7 for a full test report.

boegel · 2026-02-11T17:40:52Z

Going in, thanks @pavelToman!

Update R-bundle-CRAN-2025.11-foss-2025b.eb

8acdb6e

github-actions Bot added 2025b issues & PRs related to 2025b common toolchains change labels Jan 29, 2026

pavelToman changed the title ~~add packages R-bundle-CRAN-2025.11-foss-2025b~~ add packages to R-bundle-CRAN-2025.11-foss-2025b Jan 29, 2026

Update R-bundle-CRAN-2025.11-foss-2025b.eb

f03e01e

pavelToman mentioned this pull request Feb 2, 2026

Add smoppix to R-bundle-Bioconductor-3.22 + bump reactome.db to 1.95.0 since 1.94.0 has disappeared... #25195

Merged

Update R-bundle-CRAN-2025.11-foss-2025b.eb

93e0679

boegel added enhancement and removed change labels Feb 9, 2026

boegel added this to the next release (5.2.1?) milestone Feb 9, 2026

Thyre added the ready-to-review label Feb 10, 2026

laraPPr approved these changes Feb 11, 2026

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boegel approved these changes Feb 11, 2026

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boegel merged commit d3a5dcc into easybuilders:develop Feb 11, 2026
8 checks passed

boegel changed the title ~~add packages to R-bundle-CRAN-2025.11-foss-2025b~~ add additional extensions to to R-bundle-CRAN 2025.11 Feb 20, 2026

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