{lang}[foss/2022a] R v4.2.1

[branfosj]

(created using eb --new-pr)

[branfosj]

@boegelbot please test @ jsc-zen2

[boegelbot]

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

PR test command 'EB_PR=15767 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15767 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

• exit code: 0
• output:

Submitted batch job 1342

Test results coming soon (I hope)...

- notification for comment with ID 1165876277 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]

Test report by @branfosj
FAILED
Build succeeded for 18 out of 21 (1 easyconfigs in total)
bear-pg0105u36b.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/c23177e43e931bad8f412dd413404e88 for a full test report.

Edit: parallel extension install is not supported in a python bundle.

[boegelbot]

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/40650fc580d6bbc45ffe0564bc93a069 for a full test report.

[branfosj]

Test report by @branfosj
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in total)
bear-pg0105u36b.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/5f7455d161aecfa68584aab3db6d5aad for a full test report.

[SebastianAchilles]

Test report by @SebastianAchilles
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bdw-opensuse-154 - Linux openSUSE Leap 15.4 Alpha, x86_64, Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz (broadwell), Python 3.6.15
See https://gist.github.com/96e5c52a8b476a2d1c0b205044366dc2 for a full test report.

[SebastianAchilles]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=15767 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15767 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 8792

Test results coming soon (I hope)...

- notification for comment with ID 1166637246 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]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (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/a748766eacecc52e2ecb07eb7854a1a4 for a full test report.

[boegel]

lgtm (test report coming up)

[verdurin]

It's maybe worth mentioning here that it appears there's a problem with Seurat in that it and/or some of the projects that build on it need HDF5 <=1.8.x. I know it's in Bioconductor, but obviously that builds on what's here.

This is the upstream bug report that was mentioned to us:

mojaveazure/seurat-disk#30

Happy to open it as an issue - just wanted to mention here too.

[jfgrimm]

I'm seeing:

4366941 automake found. Running autogen.sh.                                             
4366942 + libtoolize --copy                                                             
4366943 autogen.sh: line 43: libtoolize: command not found                              
4366944 make --directory=libuv \                                                        
4366945         HAVE_DTRACE=0                    
4366946 make[1]: Entering directory `/dev/shm/jfg508/R/4.2.1/foss-2022a/httpuv/httpuv/src/libuv'
4366947 CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /dev/shm/jfg508/R/4.2.1/foss-2022a/httpuv/httpuv/src/libuv/missing aclocal-1.16 -I m4
4366948 /dev/shm/jfg508/R/4.2.1/foss-2022a/httpuv/httpuv/src/libuv/missing: line 81: aclocal-1.16: command not found            
4366949 WARNING: 'aclocal-1.16' is missing on your system.                              
4366950          You should only need it if you modified 'acinclude.m4' or              
4366951          'configure.ac' or m4 files included by 'configure.ac'.                 
4366952          The 'aclocal' program is part of the GNU Automake package:             
4366953          <https://www.gnu.org/software/automake>                                
4366954          It also requires GNU Autoconf, GNU m4 and Perl in order to run:        
4366955          <https://www.gnu.org/software/autoconf>                                
4366956          <https://www.gnu.org/software/m4/>                                     
4366957          <https://www.perl.org/>                                                
4366958 make[1]: *** [aclocal.m4] Error 127                                             
4366959 make[1]: Leaving directory `/dev/shm/jfg508/R/4.2.1/foss-2022a/httpuv/httpuv/src/libuv'
4366960 make: *** [libuv/.libs/libuv.a] Error 2                                         
4366961 ERROR: compilation failed for package httpuv

I guess we should add ('Autotools', '20220317') to builddependencies

requested changes made

[boegel]

It's maybe worth mentioning here that it appears there's a problem with Seurat in that it and/or some of the projects that build on it need HDF5 <=1.8.x. I know it's in Bioconductor, but obviously that builds on what's here.

This is the upstream bug report that was mentioned to us:

mojaveazure/seurat-disk#30

Happy to open it as an issue - just wanted to mention here too.

@verdurin Please open a separate issue for this, we've been using HDF5 1.10.x for quite some time now, so this is definitely not a reason to go back to using HDF5 1.8.x (especially since the problem is specific to Seurat).

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 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/895927443e740f0058615554c27fbd17 for a full test report.

[boegel]

lgtm

[boegel]

Going in, thanks @branfosj!