{lang}[gfbf/2023a] R v4.3.1 #18221

verdurin · 2023-06-28T16:16:46Z

(created using eb --new-pr)

verdurin · 2023-06-29T09:53:27Z

@boegelbot please test @ generoso
EB_ARGS="--skip"

boegelbot · 2023-06-29T09:55:12Z

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

PR test command 'EB_PR=18221 EB_ARGS="--skip" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18221 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11163

Test results coming soon (I hope)...

- notification for comment with ID 1612741931 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 · 2023-06-29T10:03:52Z

Test report by @boegelbot
FAILED
Build succeeded for 0 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/boegelbot/abf8a1ab4df535af074e3436ee3df68d for a full test report.

verdurin · 2023-06-29T10:28:07Z

@boegelbot please test @ generoso

boegelbot · 2023-06-29T10:30:09Z

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

PR test command 'EB_PR=18221 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18221 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11165

Test results coming soon (I hope)...

- notification for comment with ID 1612813073 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 · 2023-06-29T10:40:56Z

Test report by @boegelbot
FAILED
Build succeeded for 0 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/boegelbot/f6ddf1da85d64fdcc84d56ee157aaefb for a full test report.

verdurin · 2023-06-29T12:03:23Z

@boegelbot please test @ generoso

boegelbot · 2023-06-29T12:05:09Z

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

PR test command 'EB_PR=18221 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18221 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11167

Test results coming soon (I hope)...

- notification for comment with ID 1613023203 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 · 2023-06-29T12:32:12Z

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/boegelbot/a66244576451e64be1c9451e389c384d for a full test report.

verdurin · 2023-06-29T14:39:51Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-06-29T14:42:08Z

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

PR test command 'EB_PR=18221 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18221 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2919

Test results coming soon (I hope)...

- notification for comment with ID 1613303631 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 · 2023-06-29T15:03:52Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen2g1.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/boegelbot/0015f625f707319d990dc5a53de8e8f0 for a full test report.

fizwit · 2023-06-29T22:42:43Z

Would consider adding ggplot2? ggplot2 is a dependency 67 times in R-4.3.0.

verdurin · 2023-07-03T08:18:16Z

Would consider adding ggplot2? ggplot2 is a dependency 67 times in R-4.3.0.

What does it require?

fizwit · 2023-07-04T18:21:04Z

hmmm, ggplot2 requires 14 dependencies that are not in the current R-4.3.1. I have put ggplot2 into a new easyconfig R-Tidyverse-4.3.1 which is larger than the base R. Started with eight libraries with R-Tidyverse and processed with easy_update. The result is about 130 libraries.

easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb

verdurin · 2023-07-05T11:57:52Z

On Wed, Jul 05, 2023 at 02:55:44AM -0700, Kenneth Hoste wrote: @boegel requested changes on this pull request. > @@ -0,0 +1,374 @@ +name = 'R' +version = '4.3.1' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} Since we already have an `R` for `2022b`, shouldn't we bump this to `2023a` (once `foss/2023a` is set in stone)?

Maybe. We need it now, which is why I went with an existing toolchain.

verdurin · 2023-07-10T13:42:59Z

hmmm, ggplot2 requires 14 dependencies that are not in the current R-4.3.1. I have put ggplot2 into a new easyconfig R-Tidyverse-4.3.1 which is larger than the base R. Started with eight libraries with R-Tidyverse and processed with easy_update. The result is about 130 libraries.

Thanks. Are you happy with that approach then, rather than adding ggplot2 here?

fizwit · 2023-07-10T16:56:20Z

hmmm, ggplot2 requires 14 dependencies that are not in the current R-4.3.1. I have put ggplot2 into a new easyconfig R-Tidyverse-4.3.1 which is larger than the base R. Started with eight libraries with R-Tidyverse and processed with easy_update. The result is about 130 libraries.

Thanks. Are you happy with that approach then, rather than adding ggplot2 here?

Yes, This PR looks good to me. I am using this PR in production at the Hutch. ggplot2 is part of the Tidyverse.

For my local site, I am using this PR as the base and adding to it.
R-3.4.1 + R-Tidyverse + BioConductor = fhR

verdurin · 2023-08-11T15:58:03Z

@boegelbot please test @ generoso

boegelbot · 2023-08-11T16:00:17Z

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

PR test command 'EB_PR=18221 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18221 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11460

Test results coming soon (I hope)...

- notification for comment with ID 1675013933 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 · 2023-08-11T17:25:38Z

@verdurin: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/5834675806
Output from first failing test suite run:

FAIL: test_style_conformance (test.easyconfigs.styletests.StyleTest)
Check the easyconfigs for style
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/base/testing.py", line 97, in assertEqual
    super(TestCase, self).assertEqual(a, b)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/unittest/case.py", line 829, in assertEqual
    assertion_func(first, second, msg=msg)
AssertionError: 5 != 0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/styletests.py", line 68, in test_style_conformance
    self.assertEqual(result, 0, error_msg)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/base/testing.py", line 119, in assertEqual
    raise AssertionError("%s:\nDIFF%s:\n%s" % (msg, limit, ''.join(diff[:self.ASSERT_MAX_DIFF])))
AssertionError: There shouldn't be any code style errors (and/or warnings), found 5:
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:16:5: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:38:5: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:39:5: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:40:5: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:41:5: E265 block comment should start with '# '

: 5 != 0:
DIFF:
- 5

----------------------------------------------------------------------
Ran 17777 tests in 1133.990s

FAILED (failures=1)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

…asyconfigs into 20230628161627_new_pr_R431

boegelbot · 2023-10-23T19:25:46Z

@verdurin: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/6617574882
Output from first failing test suite run:

FAIL: test_style_conformance (test.easyconfigs.styletests.StyleTest)
Check the easyconfigs for style
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/base/testing.py", line 97, in assertEqual
    super(TestCase, self).assertEqual(a, b)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/unittest/case.py", line 829, in assertEqual
    assertion_func(first, second, msg=msg)
AssertionError: 5 != 0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/styletests.py", line 68, in test_style_conformance
    self.assertEqual(result, 0, error_msg)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/base/testing.py", line 119, in assertEqual
    raise AssertionError("%s:\nDIFF%s:\n%s" % (msg, limit, ''.join(diff[:self.ASSERT_MAX_DIFF])))
AssertionError: There shouldn't be any code style errors (and/or warnings), found 5:
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:16:5: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:38:5: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:39:5: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:40:5: E265 block comment should start with '# '
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb:41:5: E265 block comment should start with '# '

: 5 != 0:
DIFF:
- 5

----------------------------------------------------------------------
Ran 18369 tests in 1072.690s

FAILED (failures=1)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

SebastianAchilles · 2023-11-05T09:25:51Z

easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb

+    ('libjpeg-turbo', '2.1.5.1'),  # for plottting in R
+    ('LibTIFF', '4.5.0'),
+    ('Java', '11', '', SYSTEM),
+    ('libgit2', '1.7.0'),


A newer libgit2 was already merged in #18606

Suggested change

('libgit2', '1.7.0'),

('libgit2', '1.7.1'),

SebastianAchilles

@verdurin I updated to R 4.3.2, added the required dependencies and updated the extensions in verdurin#8

adding easyconfigs: R-4.3.1-gfbf-2022b.eb

08b30e9

verdurin added the update label Jun 28, 2023

Fix comment formatting

e25a4cb

Fix dependency ordering for vctrs

ae01739

More dep order fixes

6336345

verdurin closed this Jun 29, 2023

verdurin reopened this Jun 29, 2023

boegel requested changes Jul 5, 2023

View reviewed changes

easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb Outdated Show resolved Hide resolved

boegel mentioned this pull request Jul 5, 2023

R 4.3.0 vscentrum/vsc-software-stack#170

Closed

boegel added this to the release after 4.7.3 milestone Jul 6, 2023

branfosj mentioned this pull request Jul 18, 2023

{bio,lang,tools}[foss/2022b] R v4.3.1, arrow-R v11.0.0.3, R-bundle-Bioconductor v3.17 w/ R 4.3.1 #18322

Closed

verdurin changed the title ~~{lang}[gfbf/2022b] R v4.3.1~~ {lang}[gfbf/2023a] R v4.3.1 Aug 11, 2023

verdurin and others added 2 commits August 11, 2023 15:56

Change to gfbf/2023a and add missing deps

5d73ec7

Delete R-4.3.1-gfbf-2022b.eb

1110b11

libGLU was merged after I triggered the build test...

e2a1069

boegel modified the milestones: 4.8.1, release after 4.8.1 Sep 9, 2023

easybuilders deleted a comment from boegelbot Oct 23, 2023

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

f7cf39a

…asyconfigs into 20230628161627_new_pr_R431

boegel modified the milestones: next release (4.8.2), release after 4.8.2 Oct 27, 2023

boegel mentioned this pull request Nov 5, 2023

{lang}[foss/2023a] R v4.3.1 #18808

Closed

SebastianAchilles requested changes Nov 5, 2023

View reviewed changes

SebastianAchilles requested changes Nov 7, 2023

View reviewed changes

This was referenced Nov 7, 2023

{lang}[foss/2023a] R-bundle-CRAN v2023.12 #19170

Merged

{lang}[gfbf/2023a] R v4.3.2 #19185

Merged

lexming merged commit f7cf39a into easybuilders:develop Dec 9, 2023

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{lang}[gfbf/2023a] R v4.3.1 #18221

{lang}[gfbf/2023a] R v4.3.1 #18221

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{lang}[gfbf/2023a] R v4.3.1 #18221

{lang}[gfbf/2023a] R v4.3.1 #18221

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