copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command #20956

boegel · 2024-07-03T10:02:50Z

(created using eb --new-pr)

boegel · 2024-07-03T10:04:42Z

@boegelbot please test @ generoso

boegelbot · 2024-07-03T10:10:05Z

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

PR test command 'EB_PR=20956 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20956 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13873

Test results coming soon (I hope)...

- notification for comment with ID 2205644853 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 · 2024-07-03T10:13:23Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/1338158d170a4399dd4d809e71309892 for a full test report.

…sem-eval-calculate-score command

boegel · 2024-07-03T10:21:26Z

@boegelbot please test @ jsc-zen3

boegel · 2024-07-03T10:24:08Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3101.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/792cd009abcf717b341dfe171c183371 for a full test report.

boegelbot · 2024-07-03T10:30:10Z

@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=20956 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20956 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4507

Test results coming soon (I hope)...

- notification for comment with ID 2205724584 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 · 2024-07-03T10:32:41Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (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/f51343039d5e05a89340e1dbe0df59ac for a full test report.

verdurin · 2024-07-11T10:56:30Z

Appears that the sanity test command failed on jsczen3 - not immediately sure why.

verdurin · 2024-07-11T15:54:23Z

Test report by @verdurin
FAILED
Build succeeded for 5 out of 6 (1 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/33ab9769e1cacd7c631e142b9319a331 for a full test report.

verdurin · 2024-07-11T16:12:59Z

Same error for me:

== 2024-07-11 15:54:20,612 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): Sanity check failed: sanity check command rsem-eval-calculate-score --help 2>&1 | grep 'rsem-eval-calculate-score \[options\]' exited with code 1 (output: ) (at easybuild/framework/easyblock.py:3663 in _sanity_check_step)

boegel · 2024-09-11T16:13:37Z

Problem on jsc-zen3 is this:

[boegelbot@jsczen3c1 ~]$ rsem-eval-calculate-score --help
Can't locate Env.pm in @INC (you may need to install the Env module) (@INC contains: /tmp/boegelbot/software/DETONATE/1.11-GCC-12.3.0/bin /usr/local/lib64/perl5/5.32 /usr/local/share/perl5/5.32 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at /tmp/boegelbot/software/DETONATE/1.11-GCC-12.3.0/bin/rsem-eval-calculate-score line 12.

This shows we're missing a Perl dependency here too...

boegel · 2024-09-11T16:16:08Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-09-11T16:20:08Z

@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=20956 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20956 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4850

Test results coming soon (I hope)...

- notification for comment with ID 2344102821 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 · 2024-09-11T16:21:32Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3144.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/2b1d61a068494192908ff46bb73ebd09 for a full test report.

boegelbot · 2024-09-11T16:22:12Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c2.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/4581a97748fb9e84d43a18a05181c995 for a full test report.

boegel · 2024-09-11T16:26:36Z

@boegelbot please test @ generoso

boegelbot · 2024-09-11T16:30:05Z

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

PR test command 'EB_PR=20956 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20956 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14245

Test results coming soon (I hope)...

- notification for comment with ID 2344123688 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 · 2024-09-11T16:33:28Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns3 - 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/772cc82ddc167c3345715b71c3ca5418 for a full test report.

boegel added the bug fix label Jul 3, 2024

boegel added this to the release after 4.9.2 milestone Jul 3, 2024

copy missing rsem_perl_utils.pm in DETONATE, since it's required by r…

79abc87

…sem-eval-calculate-score command

boegel force-pushed the 20240703120246_new_pr_DETONATE111 branch from 95084c3 to 79abc87 Compare July 3, 2024 10:21

boegel changed the title ~~copy missing rsem_perl_utils.pm in DETONATE, since it's required by rsem-eval-calculate-score command~~ copy missing rsem_perl_utils.pm in DETONATE, since it's required by rsem-eval-calculate-score command Jul 31, 2024

boegel changed the title ~~copy missing rsem_perl_utils.pm in DETONATE, since it's required by rsem-eval-calculate-score command~~ copy missing rsem_perl_utils.pm in DETONATE, since it's required by rsem-eval-calculate-score command Jul 31, 2024

add missing Perl dependency for DETONATE v1.11

30c7c9c

bedroge approved these changes Sep 11, 2024

View reviewed changes

bedroge merged commit c6f45a8 into easybuilders:develop Sep 11, 2024
9 checks passed

boegel deleted the 20240703120246_new_pr_DETONATE111 branch September 11, 2024 19:25

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copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command #20956

copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command #20956

boegel commented Jul 3, 2024

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verdurin commented Jul 11, 2024

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boegel commented Sep 11, 2024

boegelbot commented Sep 11, 2024

boegelbot commented Sep 11, 2024

copy missing rsem_perl_utils.pm in DETONATE, since it's required by rsem-eval-calculate-score command #20956

copy missing rsem_perl_utils.pm in DETONATE, since it's required by rsem-eval-calculate-score command #20956

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boegelbot commented Sep 11, 2024

copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command #20956

copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command #20956