add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow-R 6.0.0.2 #14259

boegel · 2021-10-30T20:24:31Z

(created using eb --new-pr)

boegel · 2021-10-30T20:26:59Z

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

boegelbot · 2021-10-30T20:30:09Z

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

PR test command 'EB_PR=14259 EB_ARGS="--skip" /opt/software/slurm/bin/sbatch --job-name test_PR_14259 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7191

Test results coming soon (I hope)...

- notification for comment with ID 955588076 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 · 2021-10-30T20:50:04Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cnx1 - Linux rocky linux 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/a3a0711be61fe1ab72542184b92a4e7a for a full test report.

boegel · 2021-10-30T21:12:28Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3519.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/6aa0cd8f236ee713298d5308633dcad1 for a full test report.

branfosj · 2021-10-31T10:25:00Z

Test report by @branfosj
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/27c528e9bfef129f506019e75d453012 for a full test report.

branfosj · 2021-10-31T10:29:01Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bb-pg-login02.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz (broadwell), Python 3.6.8
See https://gist.github.com/6ef3dcff3a485c7ca56684d14992a5f4 for a full test report.

edit: This is a eb --fetch check.

easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb

…3.13 easyconfig

branfosj · 2021-10-31T11:38:55Z

Test report by @branfosj
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/d761d7ebfc0e61d07cce9e5db833e8fd for a full test report.

easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb

… easyblock Co-authored-by: Simon Branford <[email protected]>

Co-authored-by: Simon Branford <[email protected]>

branfosj · 2021-10-31T11:51:43Z

easybuild/easyconfigs/a/arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb

@@ -0,0 +1,32 @@
+easyblock = 'RPackage'
+
+name = 'arrow'


This will clash with Arrow on a lowercase module naming scheme. Possibly use arrow-R?

We should also rename https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/a/arrow/arrow-0.17.1-foss-2020a-R-4.0.0.eb

I don't consider that a problem due to the versionsuffix we're using?

If it would be a totally different "arrow", sure, but in this case it actually makes sense to have them under the same "flag"?

But, in a lowercase module naming scheme, both modules will be named arrow and contain conflict("arrow"). And, so, not be loadable at the same time. I don't think a versionsuffix solves that issue.

Though I'd not realised that we don't yet have such a scheme. See easybuilders/easybuild-framework#3199 for a proposed LowercaseEasyBuildMNS where I expect this to be problematic.

Oh right, I totally overlooked that, very good point...

That's definitely enough reason to rename to arrow-R (for lack of a better obvious name)

fixed in e6a3f2b + 67cc17f

existing arrow easyconfig renamed in #14262

boegel · 2021-10-31T11:59:28Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node2607.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/8c57e8a1214acb8ed3f17408dfe5a243 for a full test report.

boegel · 2021-10-31T12:12:26Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3519.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/ed0bb6f768a3c75972aba3522e603095 for a full test report.

boegel · 2021-10-31T13:17:34Z

@boegelbot please test @ generoso
EB_ARGS="--skip R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb"

boegelbot · 2021-10-31T13:20:09Z

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

PR test command 'EB_PR=14259 EB_ARGS="--skip R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb" /opt/software/slurm/bin/sbatch --job-name test_PR_14259 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7193

Test results coming soon (I hope)...

- notification for comment with ID 955699244 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 · 2021-10-31T13:52:26Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in total)
cnx1 - Linux rocky linux 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/a3fb84f9d8c5f885fc6ae44dc7ac086a for a full test report.

…ogether in a lowercase naming scheme

boegel · 2021-10-31T18:49:54Z

@boegelbot please test @ generoso

boegelbot · 2021-10-31T18:50:09Z

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

PR test command 'EB_PR=14259 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_14259 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7195

Test results coming soon (I hope)...

- notification for comment with ID 955772861 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 · 2021-10-31T18:52:19Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3118.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/b3da551add95a418300b488ba583ca7a for a full test report.

boegelbot · 2021-10-31T22:55:58Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
cnx1 - Linux rocky linux 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/4e1ffc65caa88e75535f93a4e06730b9 for a full test report.

branfosj · 2021-11-01T08:20:39Z

Test report by @branfosj
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/09b300b06495c6f5dcb0e59c20235835 for a full test report.

branfosj

lgtm

branfosj · 2021-11-01T08:24:02Z

Going in, thanks @boegel!

add RcisTarget extension to R-bundle-Bioconductor 3.13

d53b7a2

boegel added the enhancement label Oct 30, 2021

boegel added this to the next release (4.5.1?) milestone Oct 30, 2021

branfosj requested changes Oct 31, 2021

View reviewed changes

easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb Outdated Show resolved Hide resolved

use proper dependency for 'arrow' R library in R-bundle-Bioconductor …

32c4221

…3.13 easyconfig

boegel changed the title ~~add RcisTarget extension to R-bundle-Bioconductor 3.13~~ add RcisTarget extension to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow 6.0.0.2 R library Oct 31, 2021

branfosj requested changes Oct 31, 2021

View reviewed changes

easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb Outdated Show resolved Hide resolved

easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb Outdated Show resolved Hide resolved

easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb Outdated Show resolved Hide resolved

boegel and others added 3 commits October 31, 2021 12:41

don't enable separate_build_dir, already done by default by CMakeMake…

15ee141

… easyblock Co-authored-by: Simon Branford <[email protected]>

explicitely specify location of Python 3 installation

1652142

Co-authored-by: Simon Branford <[email protected]>

fix reference to Arrow developer documentation w.r.t. Python bindings

1bdeea9

Co-authored-by: Simon Branford <[email protected]>

branfosj requested changes Oct 31, 2021

View reviewed changes

also add NMF extension to R-bundle-Bioconductor 3.13 easyconfig

e36d48e

boegel changed the title ~~add RcisTarget extension to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow 6.0.0.2 R library~~ add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow 6.0.0.2 R library Oct 31, 2021

boegel mentioned this pull request Oct 31, 2021

{geo}[foss/2021a] SCENIC v1.2.4 #14260

Merged

use arrow-R as name for R bindings for Arrow, so they can be loaded t…

e6a3f2b

…ogether in a lowercase naming scheme

boegel changed the title ~~add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow 6.0.0.2 R library~~ add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow-R 6.0.0.2 Oct 31, 2021

fix archive source URL for arrow R package

67cc17f

branfosj mentioned this pull request Nov 1, 2021

specify to use Python provided as dependency, remove separate_build_dir, and fix URL in comment for Arrow 0.17.1 #14263

Merged

branfosj approved these changes Nov 1, 2021

View reviewed changes

branfosj merged commit 6fb6852 into easybuilders:develop Nov 1, 2021

boegel deleted the 20211030222423_new_pr_R-bundle-Bioconductor313 branch November 6, 2021 08:45

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add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow-R 6.0.0.2 #14259

add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow-R 6.0.0.2 #14259

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add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow-R 6.0.0.2 #14259

add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow-R 6.0.0.2 #14259

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