{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)

• [ ] #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: https://github.com/easybuilders/easybuild-easyconfigs/pull/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)...

*- notification for comment with ID 2195662632 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/836fe2bb479ceb9e6d0874e27e06a38f for a full test report.