{bio}[foss/2023a] HOMER v4.11 w/ R 4.3.2, libidn2 v2.3.7, wget v1.24.5 by PetrKralCZ · Pull Request #20590 · easybuilders/easybuild-easyconfigs

PetrKralCZ · 2024-05-22T12:41:11Z

(created using eb --new-pr)

PetrKralCZ · 2024-05-22T16:38:13Z

@boegelbot please test @ generoso

boegelbot · 2024-05-22T16:40:08Z

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

PR test command 'EB_PR=20590 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20590 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13514

Test results coming soon (I hope)...

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boegelbot · 2024-05-22T18:00:29Z

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/d7181fe43b7a38ee0cb29ba1c62745f7 for a full test report.

PetrKralCZ · 2024-05-22T18:15:08Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-05-22T18:20:08Z

@PetrKralCZ: 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=20590 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20590 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4173

Test results coming soon (I hope)...

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boegelbot · 2024-05-22T18:20:52Z

Test report by @boegelbot
FAILED
Build succeeded for 0 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/1e4d34394ed8ce481bd1be6c3aa09c52 for a full test report.

boegel · 2024-05-23T08:12:46Z

easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb

+    ('R-bundle-Bioconductor', '3.18', versionsuffix)
+]
+
+postinstallcmds = ["cd %(installdir)s && perl ./configureHomer.pl -install -all"]


Make sure the specific version is installed, as is done in https://github.com/bear-rsg/easybuild-easyconfigs/blob/2020a/easybuild/easyconfigs/h/HOMER/HOMER-4.11-foss-2020a.eb

boegel · 2024-05-23T09:30:26Z

@PetrKralCZ The failure on jsc-zen3 is because wget is not available, we should include that as a build dependency:

== 2024-05-23 09:28:59,436 run.py:687 INFO cmd "cd /tmp/boegelbot/pr20590/software/HOMER/4.11-foss-2023a-R-4.3.2 && perl ./configureHomer.pl -install -all" exited with exit code 0 and output:

        Current base directory for HOMER is /tmp/boegelbot/pr20590/software/HOMER/4.11-foss-2023a-R-4.3.2/./

sh: line 1: wget: command not found
        Updating Settings...
        If updating ALL, the following needs to be updated:
                SOFTWARE
                ORGANISMS
                PROMOTERS
                GENOMES

`wget -O 0.874620091010915.tmp http://homer.ucsd.edu/homer/configureHomer.pl`;
sh: line 1: wget: command not found
diff: 0.874620091010915.tmp: No such file or directory
        configureHomer.pl script is up-to-date
rm: cannot remove '0.874620091010915.tmp': No such file or directory
        Packages to Install...
                homer -> !!! Could not find homer (SOFTWARE)
        Pausing for 3 seconds (hit ctrl-C to stop)
Trouble opening /tmp/boegelbot/pr20590/software/HOMER/4.11-foss-2023a-R-4.3.2/.//bin/findMotifs.pl
readline() on closed filehandle IN at ./configureHomer.pl line 863.
mv: cannot move '.new.pl' to '/tmp/boegelbot/pr20590/software/HOMER/4.11-foss-2023a-R-4.3.2/.//bin/findMotifs.pl': No such file or directory
chmod: cannot access '/tmp/boegelbot/pr20590/software/HOMER/4.11-foss-2023a-R-4.3.2/.//bin/findMotifs.pl': No such file or directory
...

PetrKralCZ · 2024-05-23T10:50:21Z

@boegelbot please test @ generoso

boegelbot · 2024-05-23T10:55:09Z

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

PR test command 'EB_PR=20590 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20590 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13531

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 · 2024-05-23T12:18:39Z

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/341c19c2a88752a0ebba9ef9ea9709a9 for a full test report.

PetrKralCZ · 2024-05-23T12:37:42Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-05-23T12:40:08Z

@PetrKralCZ: 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=20590 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20590 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4189

Test results coming soon (I hope)...

Details

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boegelbot · 2024-05-23T12:42:25Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 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/d7af0e42e2be7fc9a2a7c3587e98e4be for a full test report.

boegel · 2024-05-24T10:56:23Z

@PetrKralCZ Last build failure shows:

        Checking for wget... /project/def-maintainers/boegelbot/rocky9/zen3/software/wget/1.24.5-GCCcore-12.3.0/bin/wget
        Checking for cut... /usr/bin/cut
        Checking for gcc... /project/def-maintainers/boegelbot/rocky9/zen3/software/GCCcore/12.3.0/bin/gcc
        Checking for g++... /project/def-maintainers/boegelbot/rocky9/zen3/software/GCCcore/12.3.0/bin/g++
        Checking for zip... which: no zip in (...)
        The program zip was not found but is strictly required
        Checking for unzip... /usr/bin/unzip
        Checking for make... /usr/bin/make
        Checking for tar... /usr/bin/tar
        Checking for gunzip... /project/def-maintainers/boegelbot/rocky9/zen3/software/gzip/1.12-GCCcore-12.3.0/bin/gunzip
        Checking for gzip... /project/def-maintainers/boegelbot/rocky9/zen3/software/gzip/1.12-GCCcore-12.3.0/bin/gzip

        Installation will halt since one or more required programs where not found.
                (or they are not in your executable path)
        Most of these programs are standard Unix Utilities that should be installed by default.
        If you are running Mac OS X, make sure to install developer tools

        Also, if you think these programs have already been installed, make sure you modify your
        configuration files to include each progam in the executable path (i.e. ~/.bash_profile)
        Refer to the Homer documentation if you need more help: http://homer.ucsd.edu/homer/

        --- Cannot Continue until required software is available ---

So you should also add Zip and UnZip as (build) depenencies.
For cut, make, tar it's typically fine to rely on OS.

PetrKralCZ · 2024-05-27T15:19:22Z

@boegelbot please test @ generoso

boegelbot · 2024-05-27T15:20:05Z

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

PR test command 'EB_PR=20590 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20590 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13570

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 · 2024-05-27T15:27:21Z

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/ba20226717d793d34d5afdf458da59ed for a full test report.

PetrKralCZ · 2024-05-27T15:38:23Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-05-27T15:40:07Z

@PetrKralCZ: 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=20590 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20590 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4223

Test results coming soon (I hope)...

Details

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boegelbot · 2024-05-27T15:43:44Z

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 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/190e3ace8efca25afbfc67dd9c83b802 for a full test report.

boegel · 2024-06-06T18:33:02Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3120.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/ed9ab082414cd5daf036b8d7d339f284 for a full test report.

boegel · 2024-06-06T18:35:06Z

Going in, thanks @PetrKralCZ!

adding easyconfigs: HOMER-4.11-foss-2023a-R-4.3.2.eb

522078b

PetrKralCZ added the new label May 22, 2024

PetrKralCZ mentioned this pull request May 22, 2024

HOMER vscentrum/vsc-software-stack#335

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boegel requested changes May 23, 2024

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PetrKralCZ added 2 commits May 23, 2024 11:57

add missing dependencies

7455540

add missing dependencies

4c00b4f

add missing build dependencies and specify installed version

4d43617

boegel added this to the 4.x milestone Jun 6, 2024

boegel changed the title ~~{bio}[foss/2023a] HOMER v4.11 w/ R 4.3.2~~ {bio}[foss/2023a] HOMER v4.11 w/ R 4.3.2, libidn2 v2.3.7, wget v1.24.5 Jun 6, 2024

boegel approved these changes Jun 6, 2024

View reviewed changes

boegel merged commit f59561d into easybuilders:develop Jun 6, 2024

boegel modified the milestones: 4.x, release after 4.9.1 Jun 6, 2024

boegel mentioned this pull request Jun 7, 2024

bump libidn2 dependency in GnuTLS 3.7.8 to v2.3.7 #20772

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PetrKralCZ commented May 22, 2024

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