{lang}[foss/2022b] R v4.2.2 by jfgrimm · Pull Request #17200 · easybuilders/easybuild-easyconfigs

jfgrimm · 2023-01-25T12:16:42Z

requires:

(created using eb --new-pr)

edit: removed extensions

Rmpi (should be fleshed out to a separate easyconfig)
ffbase: archived in CRAN

…asyconfigs into 20230125121637_new_pr_R421

boegel · 2023-02-28T18:37:36Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-02-28T18:42:08Z

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=17200 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17200 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2285

Test results coming soon (I hope)...

Details

- notification for comment with ID 1448675857 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 · 2023-02-28T18:42:30Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/425c1b24a87dd249aaae416fe792649f for a full test report.

jfgrimm · 2023-02-28T19:20:01Z

damn, forgot to update checksums

jfgrimm · 2023-02-28T19:44:32Z

should we consider dropping the archived packages? current list:

spatstat.core
unbalanced
HWxtest
diveRsity
biom
dummies
uniqueAtomMat
PoissonSeq
cghFLasso
JBTools
SDMTools
csSAM
liquidSVM
lqa
BayesPen
kedd
drugCombo
RefFreeEWAS
semPLS
gdalUtils

boegelbot · 2023-02-28T20:33:36Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/2faa585d9d7b1604d1305b91de75d955 for a full test report.

…cies

jfgrimm · 2023-03-17T12:39:48Z

@boegelbot please test @ generoso

jfgrimm · 2023-03-17T13:25:47Z

Test report by @jfgrimm
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
himem02.pri.viking.alces.network - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6130 CPU @ 2.10GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/960816a21ffd44299958e97b8c558cf5 for a full test report.

jfgrimm · 2023-03-17T15:52:45Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-03-17T15:57:08Z

@jfgrimm: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=17200 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17200 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2379

Test results coming soon (I hope)...

Details

- notification for comment with ID 1474047517 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 · 2023-03-17T16:57:18Z

Test report by @jfgrimm
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
login1.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/6a62bdd721a2318ec7ad3a59749ddd89 for a full test report.

branfosj · 2023-03-17T17:19:03Z

Test report by @branfosj
FAILED
Build succeeded for 27 out of 29 (1 easyconfigs in total)
bear-pg0104u04a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/d9b4e78934caadb3d208a8914f4df2a0 for a full test report.

branfosj · 2023-03-17T17:41:18Z

Test report by @branfosj
FAILED
Build succeeded for 27 out of 29 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux Ubuntu 20.04.2 LTS (Focal Fossa), x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.8.5
See https://gist.github.com/d574637e14aba2f4de0f7df4aa093b77 for a full test report.

boegelbot · 2023-03-17T21:28:55Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/265de1abfc98a8aa82a16c11fdf9e0b9 for a full test report.

jfgrimm · 2023-03-18T10:06:08Z

@boegelbot please test @ generoso
CORE_CNT=16
EB_ARGS="--experimental --parallel-extensions-install"

boegelbot · 2023-03-18T10:10:09Z

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

PR test command 'EB_PR=17200 EB_ARGS="--experimental --parallel-extensions-install" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17200 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10502

Test results coming soon (I hope)...

Details

- notification for comment with ID 1474803186 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).

…for R 4.2.2

requested changes in place

boegel

lgtm

branfosj · 2023-03-18T13:38:06Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0104u04b.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/ca86ca5f477c72056e0657122cc0a665 for a full test report.

branfosj · 2023-03-18T14:03:03Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u12a.bear.cluster - Linux Ubuntu 20.04.2 LTS (Focal Fossa), x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.8.5
See https://gist.github.com/9e32d1571d11c467a524c9ed4e580ac4 for a full test report.

boegel · 2023-03-18T21:33:26Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3133.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/fefcd3ecf6a1f05113d2be5a11ab311c for a full test report.

boegel · 2023-03-18T21:52:18Z

Going in, thanks @jfgrimm!

casparvl · 2023-03-19T12:36:44Z

Test report by @casparvl
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
tcn460.local.snellius.surf.nl - Linux Rocky Linux 8.7, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.6.8
See https://gist.github.com/b7c785377924ca263d40cf41fe828075 for a full test report.

jfgrimm added the update label Jan 25, 2023

jfgrimm added this to the 4.x milestone Jan 25, 2023

jfgrimm changed the title ~~{lang}[foss/2022b] R v4.2.1~~ {lang}[foss/2022b] R v4.2.2 Jan 25, 2023

adding easyconfigs: R-4.2.2-foss-2022b.eb

faf6481

jfgrimm force-pushed the 20230125121637_new_pr_R421 branch from 66f7445 to faf6481 Compare January 25, 2023 12:37

jfgrimm added 3 commits February 28, 2023 16:17

update R bundle packages

a149ef2

undo accidental changes

e306f64

add ggvenn, scatterpie, shadowtext extensions added in PRs 17043, 17125

8a8a6c9

jfgrimm modified the milestones: 4.x, next release (4.7.1?) Feb 28, 2023

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

515453c

…asyconfigs into 20230125121637_new_pr_R421

easybuilders deleted a comment from boegelbot Feb 28, 2023

fix archived packages

041d5a3

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move 'digest' package to be before filehash in the extensions list

958ea2a

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boegel modified the milestones: next release (4.7.1), release after 4.7.1 Mar 16, 2023

update package versions, fix order and add missing R package dependen…

f31ccc0

…cies

jfgrimm added 2 commits March 17, 2023 14:02

package dependencies

129ccd2

remove duplicate

a423cfb

branfosj mentioned this pull request Mar 18, 2023

specify -DPython_ROOT configure option for GDAL 3.6.2 to make sure that Python dependency is used #17560

Merged

add back useful comments + add webutils/swagger/varhandle extensions …

f62f8d8

…for R 4.2.2

branfosj previously requested changes Mar 18, 2023

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Comment thread easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb

Comment thread easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb Outdated

Comment thread easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb

branfosj reviewed Mar 18, 2023

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Comment thread easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb Outdated

Update package update date

90ea714

branfosj reviewed Mar 18, 2023

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Comment thread easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb Outdated

yesterday, not today

dbd50ab

boegel approved these changes Mar 18, 2023

View reviewed changes

boegel modified the milestones: release after 4.7.1, 4.7.1 Mar 18, 2023

This was referenced Mar 18, 2023

{data,tools}[foss/2022b,gfbf/2022b] Arrow v11.0.0, arrow-R v11.0.0.3 w/ Python 3.10.8 #17565

Merged

{bio}[foss/2022b] R-bundle-Bioconductor v3.16 #17566

Merged

boegel merged commit 1f3d1e8 into easybuilders:develop Mar 18, 2023

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jfgrimm commented Jan 25, 2023 •

edited by boegel

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