{lang}[foss/2021b] R 4.2.0 #15356

fizwit · 2022-04-27T20:54:45Z

(created using eb --new-pr)

update sanity check in R easyblock for versions >= 4.2.0, since S.h is not included anymore easybuild-easyblocks#2713

fizwit · 2022-04-27T21:04:39Z

9 new packages have been added as dependencies from updated libraries. Total exts_list is now 1053.

                  hardhat : 0.2.0 from recipes               (add) [1044, 195]
                  recipes : 0.1.17 -> 0.2.0               (update) [1044, 196]

                  weights : 1.0.4 from TraMineR              (add) [1044, 414]
                 TraMineR : 2.2-2 -> 2.2-3                (update) [1044, 415]

          spatstat.random : 2.2-0 from spatstat.core         (add) [1044, 489]
            spatstat.core : 2.3-0 -> 2.4-2                (update) [1044, 490]

                   rlemon : 0.2.0 from optmatch              (add) [1044, 697]
                 optmatch : 0.9-15 -> 0.10.0              (update) [1044, 698]

                 RSpectra : 0.16-1 from SKAT                 (add) [1044, 700]
                     SKAT : 2.0.1 -> 2.2.4                (update) [1044, 701]

                 RcppTOML : 0.1.7 from reticulate            (add) [1044, 718]
               reticulate : 1.22 -> 1.24                  (update) [1044, 719]

                  metadat : 1.2-0 from metafor               (add) [1044, 955]
                  metafor : 3.0-2 -> 3.4-0                (update) [1044, 956]

                   admisc : 0.26 from polycor                (add) [1044, 983]
                  polycor : 0.7-10 -> 0.8-1               (update) [1044, 984]

                    furrr : 0.2.3 from broom.mixed           (add) [1044, 989]
              broom.mixed : 0.2.7 -> 0.2.9.4              (update) [1044, 990]

verdurin · 2022-04-28T08:53:49Z

Test report by @verdurin
FAILED
Build succeeded for 0 out of 1 (1 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/5f21ddd36e6ecefb6a0b855284a46447 for a full test report.

verdurin · 2022-04-28T08:55:20Z

Checksum error (of course):

== 2022-04-28 08:53:47,405 filetools.py:1306 DEBUG Computed sha256 checksum for /eb/maint/sources/r/R/extensions/rda_1.0.2-2.1.tar.gz: 6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8 (correct checksum: eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e)
== 2022-04-28 08:53:47,420 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): Checksum verification for extension source rda_1.0.2-2.1.tar.gz failed (at easybuild/framework/easyblock.py:640 in collect_exts_file_info)

fizwit · 2022-04-29T19:12:18Z

rda and AnalyzeFMRI been removed from CRAN. This might be due to the fact that there are build issues and the maintainers have not updated the packages to reflect that they have not tested with 4.2. The packages could re-emerge as the authors fix deficiencies. I'm not sure how to handle these packages, they were available when I started working with 4.2 but have since been pulled. rda is available from the archives.

branfosj

These suggested changes:

restores comments that --inject-checksums removes
add an alternative checksum for rda
add and update recently added packages
remove AnalyzeFMRI as it has src/spatial.filters.non.linear.c has #include <S.h>

easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb

…or rda, remove AnalyzeFMRI

easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb

branfosj · 2022-05-04T06:07:23Z

@boegelbot please test @ generoso

boegelbot · 2022-05-04T06:10:09Z

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

PR test command 'EB_PR=15356 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15356 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 8486

Test results coming soon (I hope)...

Details

- notification for comment with ID 1116958801 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).

branfosj · 2022-05-04T09:40:06Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.5, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/88e4160050c6138f9d37d523a10f76ad for a full test report.

boegelbot · 2022-05-04T12:32:48Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/b04d063cc513784c7f510b119f1473b3 for a full test report.

changes made

boegel · 2022-05-04T16:19:38Z

@boegelbot please test @ jsc-zen2
EB_ARGS="--parallel-extensions-install --experimental"

boegelbot · 2022-05-04T16:22:10Z

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

PR test command 'EB_PR=15356 EB_ARGS="--parallel-extensions-install --experimental" /opt/software/slurm/bin/sbatch --job-name test_PR_15356 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 1165

Test results coming soon (I hope)...

Details

- notification for comment with ID 1117549633 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

lgtm after visual review, I'll await result from the test installs I've kickstarted, but should be good to go...

verdurin · 2022-05-04T18:17:46Z

Test report by @verdurin
FAILED
Build succeeded for 0 out of 1 (1 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/ef871a06aa75a4117e6d9e4ee4c45ae6 for a full test report.

boegelbot · 2022-05-04T18:20:30Z

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/d62186d2e322e949844b38a27a01cb33 for a full test report.

boegel · 2022-05-04T22:10:35Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node2602.swalot.os - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/5f6a05e2f30abfe12a8eff70f6804292 for a full test report.

boegel · 2022-05-05T06:23:40Z

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node3119.skitty.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/8252d5ecf7e5779bd69f720d9445eb20 for a full test report.

boegel · 2022-05-05T06:30:51Z

My test reports were running with an outdated easyblocks installation that didn't include easybuilders/easybuild-easyblocks#2713 yet; likewise for @verdurin

I'll upload a new test report with --module-only after updating my easyblocks installation, and then get this merged.

boegel · 2022-05-05T08:17:09Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node2602.swalot.os - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/a3acebd4bb1aedc7c975f2e73f0f84b8 for a full test report.

boegel · 2022-05-05T08:37:41Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3102.skitty.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/096ae750629bd9069c2239be7fd1011a for a full test report.

boegel · 2022-05-05T10:15:09Z

Going in, thanks @fizwit!

verdurin · 2022-05-06T12:56:36Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 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/87913fad3c165805d2d8fe46630271bf for a full test report.

fizwit · 2022-05-06T20:11:54Z

thanks, @boegel @verdurin @branfosj for the help.
I have contacted the maintainers of AnalyzeFMRI with the patch and they have responded. I hope that it makes it back into CRAN.

boegel · 2022-05-09T07:31:41Z

@fizwit You have a patch for AnalyzeFMRI which makes it compatible with R v4.2.0?
If so, why don't we use that to add AnalyzeFMRI back as extension?

{langg}[foss/2021b] R 4.2.0

972fbef

jfgrimm changed the title ~~{langg}[foss/2021b] R 4.2.0~~ {lang}[foss/2021b] R 4.2.0 Apr 29, 2022

branfosj added the update label May 3, 2022

branfosj previously requested changes May 3, 2022

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branfosj reviewed May 3, 2022

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easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb Outdated Show resolved Hide resolved

boegel added this to the 4.x milestone May 3, 2022

restore comments, restore recently added packages, add alt checksum f…

042145d

…or rda, remove AnalyzeFMRI

branfosj reviewed May 4, 2022

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easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb Show resolved Hide resolved

add alt checksums for rda

e25b2fb

easybuilders deleted a comment from boegelbot May 4, 2022

boegel modified the milestones: 4.x, next release (4.5.5?) May 4, 2022

boegel approved these changes May 4, 2022

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boegel merged commit 485e357 into easybuilders:develop May 5, 2022

{lang}[foss/2021b] R 4.2.0 #15356

{lang}[foss/2021b] R 4.2.0 #15356

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fizwit commented Apr 27, 2022 •

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