{bio,tools}[foss/2023b] arrow-R v16.1.0, R-bundle-Bioconductor v3.19 w/ R 4.4.1

[branfosj]

(created using eb --new-pr)

• {lang}[foss/2023b,gfbf/2023b] R v4.4.1, R-bundle-CRAN v2024.06 #20898

[bedroge]

@branfosj Note that this seems to be based on https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/a/arrow-R/arrow-R-14.0.1-foss-2023a-R-4.3.2.eb, where I used the full Arrow source tarball instead of the CRAN tarball. This was because we needed a specific version that was not available on CRAN, see: #20324.

Other/older versions do use the CRAN releases, e.g. https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb.

I'm not sure what we should prefer and if it really matters, from what I remember the CRAN tarballs just contain the R interface and some files differ a bit, mostly in style-related things. This version is available on CRAN, so perhaps we could/should stick to that one again?

[branfosj]

@branfosj Note that this seems to be based on https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/a/arrow-R/arrow-R-14.0.1-foss-2023a-R-4.3.2.eb, where I used the full Arrow source tarball instead of the CRAN tarball. This was because we needed a specific version that was not available on CRAN, see: #20324.

Other/older versions do use the CRAN releases, e.g. https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb.

I'm not sure what we should prefer and if it really matters, from what I remember the CRAN tarballs just contain the R interface and some files differ a bit, mostly in style-related things. This version is available on CRAN, so perhaps we could/should stick to that one again?

Changed in 40baa44

[branfosj]

Code I used to check for duplicate extensions between the easyconfigs:

from easybuild.framework.easyconfig.easyconfig import EasyConfig
from easybuild.tools.options import set_up_configuration

set_up_configuration(reconfigure=True)

r = EasyConfig('R-4.4.1-gfbf-2023b.eb', validate=False)
r_cran = EasyConfig('R-bundle-CRAN-2024.06-foss-2023b.eb', validate=False)
r_bio = EasyConfig('R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb', validate=False)

r_exts = []
r_cran_exts = []
r_bio_exts = []

for ext in r['exts_list']:
    if isinstance(ext, tuple):
        r_exts.append(ext[0])

for ext in r_cran['exts_list']:
    if isinstance(ext, tuple):
        r_cran_exts.append(ext[0])

for ext in r_bio['exts_list']:
    if isinstance(ext, tuple):
        r_bio_exts.append(ext[0])

list(set(r_exts) & set(r_cran_exts))
list(set(r_exts) & set(r_bio_exts))
list(set(r_bio_exts) & set(r_cran_exts))

[branfosj]

Test report by @branfosj
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
bear-pg0210u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8480CL (sapphirerapids), Python 3.6.8
See https://gist.github.com/branfosj/319c110afcae8260e8e56077353fabe7 for a full test report.

[branfosj]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=20913 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20913 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 13845

Test results coming soon (I hope)...

Details

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Message to humans: this is just bookkeeping information for me,
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[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - 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/836fe2bb479ceb9e6d0874e27e06a38f for a full test report.

[Flamefire]

The dependencies have been merged. Can you sync this branch please @branfosj

[Flamefire]

Test report by @Flamefire
FAILED
Build succeeded for 74 out of 77 (2 easyconfigs in total)
i7150 - Linux Rocky Linux 8.9 (Green Obsidian), x86_64, AMD EPYC 7702 64-Core Processor (zen2), Python 3.8.17
See https://gist.github.com/Flamefire/bdb75961ea4f712d2eaf5cdac37b5362 for a full test report.

[boegel]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=20913 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20913 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 14421

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).

[boegel]

@boegelbot please test @ jsc-zen3

[boegelbot]

@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=20913 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20913 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5023

Test results coming soon (I hope)...

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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]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - 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/7071c95ce6858c0cbb5c593a63741723 for a full test report.

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 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/887d64098cbe3670d39e7b3cfffc77c4 for a full test report.

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3113.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/533d84cabd49ea5857e095372e181b84 for a full test report.

[boegel]

@boegelbot please test @ jsc-zen3

[boegelbot]

@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=20913 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20913 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5059

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]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 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/2c357422598aa6bb5910e9ead6d19b62 for a full test report.

[Flamefire]

Test report by @Flamefire
FAILED
Build succeeded for 0 out of 2 (2 easyconfigs in total)
i7005 - Linux Rocky Linux 8.9 (Green Obsidian), x86_64, AMD EPYC 7702 64-Core Processor (zen2), Python 3.8.17
See https://gist.github.com/Flamefire/5582893e68a420cc6b0278fd4d1ef73e for a full test report.

[boegel]

@Flamefire Looks like your ImageMagick/7.1.1-34-GCCcore-13.2.0 module disappeared, which is required by R-bundle-CRAN/2024.06-foss-2023b...

I won't let that block this PR, the test report from the bot is good enough imho

[boegel]

lgtm

[boegel]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=20913 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20913 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 14459

Test results coming soon (I hope)...

Details

- notification for comment with ID 2407852550 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]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - 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/49945a345d3f0fb315a63f1062b2b573 for a full test report.

[boegel]

Going in, thanks @branfosj!

[Flamefire]

@Flamefire Looks like your ImageMagick/7.1.1-34-GCCcore-13.2.0 module disappeared, which is required by R-bundle-CRAN/2024.06-foss-2023b...

Yeah I was testing on another cluster that hasn't have that installed yet and installing fails due to missing library paths which I thought I had fixed somewhere already. Got to check why it reappeared.

Turns out I only fixed it for the 13.3 version: https://github.com/easybuilders/easybuild-easyconfigs/pull/21386/files#diff-204f778b98c53d5b87f6ee5e34a3262ed719430c961faa7bea7dc9b9dd70b2e7
According to my comment the ConfigureMake built Harfbuzz for 13.2 should work. Maybe the dependencies have been moved making the paths wrong. I'll add a PR to fix this for all recent-ish ImageMagick versions

Done in #21640