{bio}[foss/2025a] R-bundle-Bioconductor v3.22 w/ R 4.5.1

[SIB-software]

(created using eb --new-pr)

[smoretti]

Requires

• {tools}[foss/2025a] arrow-R v22.0.0 w/ R 4.5.1 #24506
• {lang}[foss/2025a] R-bundle-CRAN v2025.10 #24389

Based on #24469 eb file

@smoretti i updated this comment so it shows the status of the PRs

[smoors]

closing and reopening to force a resync..

[github-actions]

Diff of new easyconfig(s) against existing ones is too long for a GitHub comment. Use --review-pr (and --review-pr-filter / --review-pr-max) locally.

[smoors]

@boegelbot please test @ jsc-zen3

[boegelbot]

@smoors: 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=24626 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24626 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 8886

Test results coming soon (I hope)...

Details

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it is of no use to you (unless you think I have a bug, which I don't).

[smoors]

i'm seeing some R-packages in the 2024a version that are missing here, can you add them back?

• ccmap
• cummeRbund
• DeconRNASeq
• hiAnnotator
• Maaslin2
• Repitools
• rGADEM
• rols
• struct
• structToolbox
• zlibbioc

[smoretti]

@smoors I followed what @branfosj mentioned in #24469.
Those packages are "Removed because deprecated and not available" or "Remove because they are not currently being distributed for Bioconductor 3.22"

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (total: 7 hours 41 mins 43 secs) (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/a8f7d1cba8539460d3bbfb78d6e03e6c for a full test report.

[smoors]

@smoors I followed what @branfosj mentioned in #24469. Those packages are "Removed because deprecated and not available" or "Remove because they are not currently being distributed for Bioconductor 3.22"

thanks, i missed that. would be good to mention such things in the PR description.

[smoors]

lgtm