{bio,tools}[foss/2022a] R-bundle-Bioconductor v3.15, arrow-R v8.0.0 by branfosj · Pull Request #15829 · easybuilders/easybuild-easyconfigs

branfosj · 2022-07-07T18:19:03Z

(created using eb --new-pr)

… arrow-R-8.0.0-foss-2022a-R-4.2.1.eb

branfosj · 2022-07-07T18:57:28Z

@boegelbot please test @ generoso

boegelbot · 2022-07-07T19:00:12Z

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

PR test command 'EB_PR=15829 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15829 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 8843

Test results coming soon (I hope)...

Details

- notification for comment with ID 1178081800 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 · 2022-07-07T20:45:03Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/5181be6a3029ac3c4a4b1fb3489aa43a for a full test report.

boegel · 2022-07-07T21:43:18Z

Test report by @boegel
FAILED
Build succeeded for 5 out of 6 (3 easyconfigs in total)
node3108.skitty.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/5bb8887b2948a81c6175d5b7fce3c6fb for a full test report.

jfgrimm · 2022-07-07T22:19:54Z

Test report by @jfgrimm
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in total)
node022.pri.viking.alces.network - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6138 CPU @ 2.00GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/2fed535dd0112b8bc291dc35d97206d2 for a full test report.

branfosj · 2022-07-08T04:47:41Z

Test report by @branfosj
FAILED
Build succeeded for 3 out of 4 (3 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/15054c3d9917bd7eabecaa72f4785dba for a full test report.

branfosj · 2022-07-08T07:32:35Z

Error is the same as in #11104 and that was fixed by adding pkg-config as a builddep. I.e. error of:

OsiAuxInfo.cpp:10:10: fatal error: CoinPragma.hpp: No such file or directory
   10 | #include "CoinPragma.hpp"
      |          ^~~~~~~~~~~~~~~~
compilation terminated.

with a -I/tmp/Rtmp48WLPH/Rbuild56dab4bdb9c69/lpsymphony/src/SYMPHONY/include/coin being there.

branfosj · 2022-07-08T10:00:54Z

Working on a easyconfig with a reduced set of extensions:

fails with pkgconf as a build dep
builds with pkg-config as a build dep

branfosj · 2022-07-08T10:53:34Z

@boegelbot please test @ generoso

boegelbot · 2022-07-08T10:55:09Z

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

PR test command 'EB_PR=15829 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15829 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 8849

Test results coming soon (I hope)...

Details

- notification for comment with ID 1178847583 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).

jfgrimm · 2022-07-08T15:03:55Z

@branfosj alternatively, perhaps we should point it at the easybuild-built Coin, rather than letting it build its own?

boegelbot · 2022-07-08T15:51:56Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/13aa07522c439472a3749a5e77a04b2d for a full test report.

boegel · 2022-07-09T08:33:57Z

easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb

+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [('pkg-config', '0.29.2')]


@branfosj Please add a clear comment why we're sticking to pkg-config here rather than using pkgconf.

We should also try and figure out why pkgconf isn't working as expected, since it's intended to be a drop-in replacement.
It may have something to do with exit codes of pkgconf vs pkg-config (see also easybuilders/easybuild-easyblocks#2736)

Ping @branfosj

With 685cdf8 and e92925f I've added explanations into R-bundle-Bioconductor and pkg-config as to why this is being used.

I've been unable to work out how to fix the R package to build with pkgconf.

verdurin · 2022-07-12T16:54:05Z

Test report by @verdurin
SUCCESS
Build succeeded for 4 out of 4 (4 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/f4dd7ac46aad72b9928b665f93d4fecf for a full test report.

…le-Bioconductor315

…asyconfigs into 20220707191857_new_pr_R-bundle-Bioconductor315

…ss/2022a

boegel · 2022-09-10T13:34:01Z

@boegelbot please test @ generoso

boegelbot · 2022-09-10T13:35:10Z

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

PR test command 'EB_PR=15829 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15829 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 9145

Test results coming soon (I hope)...

Details

- notification for comment with ID 1242730180 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 · 2022-09-10T18:01:10Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/8cbdaaa1eb3fc5d213ce00c367dae318 for a full test report.

boegel · 2022-09-10T19:50:29Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3114.skitty.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/b69bdee1110f574ac2433d99678da448 for a full test report.

boegel

lgtm

boegel · 2022-09-10T20:53:31Z

Going in, thanks @branfosj!

adding easyconfigs: R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb,…

ba8b56c

… arrow-R-8.0.0-foss-2022a-R-4.2.1.eb

branfosj added the update label Jul 7, 2022

boegel added this to the 4.x milestone Jul 7, 2022

add Arrow in 2022a

a4a5991

use pkg-config instead of pkgconf for R-bundle-Bioconductor

2320f36

boegel reviewed Jul 9, 2022

View reviewed changes

boegel modified the milestones: 4.x, next release (4.6.1?) Jul 9, 2022

branfosj and others added 5 commits August 31, 2022 09:16

Merge branch 'easybuilders:develop' into 20220707191857_new_pr_R-bund…

7a75d42

…le-Bioconductor315

explain use of pkg-config instead of pkgconf

685cdf8

redirect to pkgconf and explain why this pkg-config is here

e92925f

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

ce12fe7

…asyconfigs into 20220707191857_new_pr_R-bundle-Bioconductor315

stick to HDF5 v1.12.2 as dependency for R-bundle-Bioconductor with fo…

7a96c15

…ss/2022a

boegel approved these changes Sep 10, 2022

View reviewed changes

boegel merged commit 14d05b4 into easybuilders:develop Sep 10, 2022

branfosj deleted the 20220707191857_new_pr_R-bundle-Bioconductor315 branch September 11, 2022 02:56


		toolchain = {'name': 'foss', 'version': '2022a'}

		builddependencies = [('pkg-config', '0.29.2')]

Conversation

branfosj commented Jul 7, 2022

Uh oh!

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