{bio,tools}[foss/2025b] arrow-R v22.0.0, R-bundle-Bioconductor v3.22 w/ R 4.5.2

[branfosj]

(created using eb --new-pr)

• {lang}[gfbf/2025b] R v4.5.2 #24318
• {data}[gfbf/2025b] Arrow v22.0.0 #24463
• {lang}[foss/2025b] R-bundle-CRAN v2025.11 #24465

Removed because deprecated and not available

• zlibbioc: https://www.bioconductor.org/packages/3.21/bioc/html/zlibbioc.html
• hiAnnotator: https://bioconductor.org/packages/3.22/bioc/html/hiAnnotator.html
• ccmap: https://bioconductor.org/packages/3.22/bioc/html/ccmap.html
• Repitools: https://bioconductor.org/packages/3.22/bioc/html/Repitools.html
• rGADEM: https://bioconductor.org/packages/3.22/bioc/html/rGADEM.html

Remove because they are not currently being distributed for Bioconductor 3.22

On the page for each see that the 'Source Package' is empty. If a .tar.gz appears there then they are available again.

• cummeRbund: https://bioconductor.org/packages/3.22/bioc/html/cummeRbund.html
• DeconRNASeq: https://bioconductor.org/packages/3.22/bioc/html/DeconRNASeq.html
• rols: https://bioconductor.org/packages/3.22/bioc/html/rols.html
• struct: https://bioconductor.org/packages/3.22/bioc/html/struct.html
• structToolbox: https://bioconductor.org/packages/3.22/bioc/html/structToolbox.html
• Maaslin2: https://bioconductor.org/packages/3.22/bioc/html/Maaslin2.html

[branfosj]

Test report by @branfosj
SUCCESS
Build succeeded for 2 out of 2 (total: 8 hours 50 mins 12 secs) (2 easyconfigs in total)
bear-pg0210u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8480CL (sapphirerapids), Python 3.6.8
See https://gist.github.com/branfosj/176ecf2ef72d14344053eb1ac6ca8d04 for a full test report.

[SebastianAchilles]

@boegelbot please test @ jsc-zen3
CORE_CNT=16

[boegelbot]

@SebastianAchilles: 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=24469 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24469 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 8850

Test results coming soon (I hope)...

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

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (total: 8 hours 14 mins 20 secs) (2 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/1a6c03827c2aa50c0ed193920d04f00e for a full test report.

[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.

[Thyre]

Test report by @Thyre
SUCCESS
Build succeeded for 2 out of 2 (total: 1 hour 57 mins 43 secs) (2 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.6, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 580.95.05, Python 3.9.21
See https://gist.github.com/Thyre/64703f88053453b25a4a7048654463d7 for a full test report.

[boegel]

lgtm

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (total: 3 hours 16 mins 51 secs) (2 easyconfigs in total)
node4208.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/ae738d0575cce7e16409d3f3bf84fd45 for a full test report.

[boegel]

Going in, thanks @branfosj!