{bio}[foss/2023a] R-bundle-Bioconductor v3.18, arrow-R v14.0.0.2, semla v1.1.6 w/ R 4.3.2 by NPotvin · Pull Request #19747 · easybuilders/easybuild-easyconfigs

NPotvin · 2024-01-30T13:39:33Z

(created using eb --new-pr)

… arrow-R-14.0.0.2-foss-2023a-R-4.3.2.eb, semla-1.1.6-foss-2023a-R-4.3.2.eb

NPotvin · 2024-01-30T14:03:21Z

Hello,

If trying to install the Bioconductor bundle, it will most probably fail on downloading the source for RcisTarget.
there is an open issue on the git repo of RcisTarget here

For now, the way to install the bundle is by manually downloading the tar from here so easybuild can find it localy

verdurin · 2024-02-01T17:25:10Z

Test report by @verdurin
FAILED
Build succeeded for 4 out of 6 (3 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/82add065edec93d9050fa2829ae0b788 for a full test report.

verdurin · 2024-02-01T17:33:22Z

Failure above is expected, just thought I'd try it anyway.

boegel · 2024-02-01T17:55:19Z

@NPotvin I've included a fix for the RcisTarget download issue in 855a923 .
Downside of that approach is that we can't include a SHA256 checksum, because the source tarball obtained via https://code.bioconductor.org/browse/RcisTarget/RELEASE_3_18 seems to be generated on the fly (so it's slightly different every time, without the contents being different).

That should fix the problem though, and make this good to go.

I've done a comparison with the existing R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb, and all changes relative to it made sense to me...

Thanks a lot for your efforts on this!

boegel · 2024-02-01T17:55:26Z

@boegelbot please test @ generoso

boegelbot · 2024-02-01T18:00:05Z

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

PR test command 'EB_PR=19747 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19747 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12810

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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boegel · 2024-02-01T18:02:58Z

@boegelbot please test @ jsc-zen3

branfosj · 2024-02-01T18:07:54Z

That should fix the problem though, and make this good to go.

The reason for there being no download listed against 'Source Package' at https://bioconductor.org/packages/release/bioc/html/RcisTarget.html is because there is a build failure: https://bioconductor.org/checkResults/release/bioc-LATEST/RcisTarget/nebbiolo2-checksrc.html

Package 'zoo' is required to calculate the aproximate RCC distributions.To install it, run:	 install.packages('zoo')

and that is confusing as zoo is in the list of packages in that environment: https://bioconductor.org/checkResults/release/bioc-LATEST/nebbiolo2-R-instpkgs.html

boegelbot · 2024-02-01T18:10:08Z

@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=19747 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_19747 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 3546

Test results coming soon (I hope)...

Details

- notification for comment with ID 1921908848 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).

boegel · 2024-02-01T18:28:15Z

That should fix the problem though, and make this good to go.

The reason for there being no download listed against 'Source Package' at https://bioconductor.org/packages/release/bioc/html/RcisTarget.html is because there is a build failure: https://bioconductor.org/checkResults/release/bioc-LATEST/RcisTarget/nebbiolo2-checksrc.html
Package 'zoo' is required to calculate the aproximate RCC distributions.To install it, run:	 install.packages('zoo')
and that is confusing as zoo is in the list of packages in that environment: https://bioconductor.org/checkResults/release/bioc-LATEST/nebbiolo2-R-instpkgs.html

@branfosj Maybe good to point that out in aertslab/RcisTarget#39

boegelbot · 2024-02-01T21:38:35Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 3 (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/98bb2d1728d1fc863b2197b7dca27dfb for a full test report.

boegelbot · 2024-02-01T22:01:27Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 3 (3 easyconfigs in total)
cns2 - 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/a72de21900a2ee9e8bcf0297b13403cd for a full test report.

boegel · 2024-02-02T00:11:06Z

Test report by @boegel
FAILED
Build succeeded for 1 out of 3 (3 easyconfigs in total)
node3161.skitty.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/boegel/b8aa34e91785d79bcc9f7a14cebbc606 for a full test report.

boegel · 2024-02-02T08:42:20Z

problem with RcisTarget sources fixed in 1413fdc

boegel · 2024-02-02T08:42:51Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-02-02T08:50:08Z

@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=19747 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_19747 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 3548

Test results coming soon (I hope)...

Details

- notification for comment with ID 1923337597 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).

boegel · 2024-02-02T10:30:52Z

@boegelbot please test @ generoso

boegelbot · 2024-02-02T10:35:08Z

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

PR test command 'EB_PR=19747 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19747 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12813

Test results coming soon (I hope)...

Details

- notification for comment with ID 1923522682 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 · 2024-02-02T12:38:45Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/af0636009491e4b38dc53418b37ba2a5 for a full test report.

boegelbot · 2024-02-02T15:26:11Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 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/2e69037b2f5a725d019bd35534d4861f for a full test report.

boegel · 2024-02-02T17:24:00Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3161.skitty.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/boegel/8235fe505edeea0912657a9430d765fd for a full test report.

boegel

lgtm

boegel · 2024-02-06T09:48:13Z

Going in, thanks @NPotvin!

adding easyconfigs: R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb,…

88a1b6b

… arrow-R-14.0.0.2-foss-2023a-R-4.3.2.eb, semla-1.1.6-foss-2023a-R-4.3.2.eb

boegel added the update label Feb 1, 2024

boegel added this to the release after 4.9.0 milestone Feb 1, 2024

fix download of RcisTarget 1.22.0 in R-bundle-Bioconductor 3.18

855a923

RcisTarget sources is .tar, not .tar.gz

1413fdc

boegel approved these changes Feb 6, 2024

View reviewed changes

boegel merged commit e5e4ca7 into easybuilders:develop Feb 6, 2024

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NPotvin commented Jan 30, 2024

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