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use *DESCRIPTION rather than */DESCRIPTION in RPackage.requires_deps#3490

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Micket merged 1 commit intoeasybuilders:5.0.xfrom
boegel:20241016140823_new_pr_rpackage
Oct 17, 2024
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use *DESCRIPTION rather than */DESCRIPTION in RPackage.requires_deps#3490
Micket merged 1 commit intoeasybuilders:5.0.xfrom
boegel:20241016140823_new_pr_rpackage

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@boegel boegel commented Oct 16, 2024 •
edited by akesandgren
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(created using eb --new-pr)

The DESCRIPTION file is not always in a subdirectory in the tarball, RcisTarget_1.22.0.tar is a example of that.

We can get rid of that assumption by simply using *DESCRIPTION, which works fine regardless of whether the DESCRIPTION file is in a subdirectory or not:

$ tar tfv RcisTarget_1.22.0.tar  | grep DESC
-rw-rw-r-- root/root      1918 2024-02-02 09:32 DESCRIPTION

$ tar --wildcards --extract --file RcisTarget_1.22.0.tar --to-stdout '*/DESCRIPTION'
tar: */DESCRIPTION: Not found in archive
tar: Exiting with failure status due to previous errors
$ echo $?
2

$ tar --wildcards --extract --file RcisTarget_1.22.0.tar --to-stdout '*DESCRIPTION' | head -2
Package: RcisTarget
Type: Package

$ tar tfvz DESeq2_1.44.0.tar.gz | grep DESCR
-rw-r--r-- biocbuild/biocbuild 2119 2024-05-01 05:29 DESeq2/DESCRIPTION

$ tar --wildcards --extract --file DESeq2_1.44.0.tar.gz  --to-stdout '*DESCRIPTION' | head -2
Package: DESeq2
Type: Package

@boegel boegel mentioned this pull request Oct 16, 2024
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@boegel boegel added bug fix EasyBuild-5.0 EasyBuild 5.0 labels Oct 16, 2024
@boegel boegel added this to the 5.0 milestone Oct 16, 2024
@boegel boegel changed the title use '*DESCRIPTION' rather than '*/DESCRIPTION' in RPackage.requires_deps use *DESCRIPTION rather than */DESCRIPTION in RPackage.requires_deps Oct 16, 2024
@boegel boegel mentioned this pull request Oct 16, 2024
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boegel commented Oct 16, 2024 •
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@boegelbot please test @ jsc-zen3
EB_ARGS="R-4.4.1-gfbf-2023b.eb --parallel-extensions-install --experimental --installpath /tmp/$USER/pr3490"
EB_BRANCH=5.0.x
CORE_CNT=16

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boegelbot commented Oct 16, 2024

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ "5.0.x" != 'develop' ]]; then EB_BRANCH="5.0.x" ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/"5.0.x" source init_env_easybuild_develop.sh; fi; EB_PR=3490 EB_ARGS="R-4.4.1-gfbf-2023b.eb --parallel-extensions-install --experimental --installpath /tmp/$USER/pr3490" EB_REPO=easybuild-easyblocks EB_BRANCH="5.0.x" /opt/software/slurm/bin/sbatch --job-name test_PR_3490 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5089

Test results coming soon (I hope)...

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boegelbot commented Oct 16, 2024

Test report by @boegelbot

Overview of tested easyconfigs (in order)

  • SUCCESS R-4.4.1-gfbf-2023b.eb

Build succeeded for 1 out of 1 (1 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/0d58456f20409501a6c4b9b933c066d9 for a full test report.

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boegel commented Oct 16, 2024

Test report by @boegel

Overview of tested easyconfigs (in order)

  • SUCCESS R-4.4.1-gfbf-2023b.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3508.doduo.os - Linux RHEL 8.8, x86_64, AMD EPYC 7552 48-Core Processor, Python 3.6.8
See https://gist.github.com/boegel/346d4f240832e428e829f3f604800706 for a full test report.

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lgtm

@Micket Micket merged commit eeda121 into easybuilders:5.0.x Oct 17, 2024
@boegel boegel deleted the 20241016140823_new_pr_rpackage branch October 17, 2024 09:03
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boegel commented Oct 17, 2024

Test report by @boegel

Overview of tested easyconfigs (in order)

  • SUCCESS R-bundle-CRAN-2024.06-foss-2023b.eb
  • SUCCESS arrow-R-16.1.0-foss-2023b-R-4.4.1.eb
  • SUCCESS R-bundle-Bioconductor-3.19-foss-2023b-R-4.4.1.eb

Build succeeded for 3 out of 3 (1 easyconfigs in total)
node3508.doduo.os - Linux RHEL 8.8, x86_64, AMD EPYC 7552 48-Core Processor, Python 3.6.8
See https://gist.github.com/boegel/1af6586ab392fcc2d491841b299c4c27 for a full test report.

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