{bio,math}[foss/2021a] R-bundle-Bioconductor v3.13, ncdf4 v1.17

[branfosj]

(created using eb --new-pr)

Requires:

• R ({lang}[foss/2021a] R v4.1.0 #13032)
• netCDF ({data}[foss/2021a] GDAL v3.3.0, GEOS v3.9.1, HDF v4.2.15, ... w/ Python 3.9.5 #13030)
• Boost ({devel}[GCC/10.3.0,intel-compilers/2021.2.0] Boost v1.76.0 #12977)

Download fails for these so they've been removed:

• genoset (1.48.0) - Bioconductor page shows build failure and lists package as deprecated (https://bioconductor.org/packages/release/bioc/html/genoset.html)
• SSPA (2.32.1) - Bioconductor page shows build failure and lists package as deprecated (https://bioconductor.org/packages/release/bioc/html/SSPA.html)
• KEGGprofile (1.34.0) - Bioconductor page shows build failure (https://bioconductor.org/packages/release/bioc/html/KEGGprofile.html)

[branfosj]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=13044 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_13044 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 17781

Test results coming soon (I hope)...

- notification for comment with ID 880545159 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
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
generoso-c1-s-2 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/d228ded6298a00dfd8b0466b8b5716fa for a full test report.

[verdurin]

Test report by @verdurin
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
nuc.lan - Linux Fedora 33, x86_64, Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, Python 3.9.5
See https://gist.github.com/65227c8332ea5a3bf75592a1f7204fa7 for a full test report.

[branfosj]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=13044 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_13044 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 17782

Test results coming soon (I hope)...

- notification for comment with ID 880563027 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).

[verdurin]

Test report by @verdurin
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
nuc.lan - Linux Fedora 33, x86_64, Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, Python 3.9.5
See https://gist.github.com/347e2156be302e983f5c5de7b841f48e for a full test report.

[verdurin]

Test report by @verdurin
FAILED
Build succeeded for 0 out of 1 (2 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/c3fc9f9c052b766dbaf42acb77661a24 for a full test report.

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
generoso-c1-s-2 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/4d74b4c6cc02a460b90cc789ea33c0fd for a full test report.

[verdurin]

Test report by @verdurin
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
nuc.lan - Linux Fedora 33, x86_64, Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, Python 3.9.5
See https://gist.github.com/fdf5d893c74c3e0a2400ed69ca80091b for a full test report.

[branfosj]

Test report by @branfosj
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
bear-pg0211u08b.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/28d1db382efed922d49e0f7f60d3fb9d for a full test report.

[verdurin]

Test report by @verdurin
FAILED
Build succeeded for 0 out of 1 (2 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/ecd720fcad12f1307f4322df70cf9821 for a full test report.

[branfosj]

Test report by @branfosj
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
bear-pg0211u08b.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/388474afa3ca19a78211866c1bb52164 for a full test report.

[smoors]

Test report by @smoors
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
node374.hydra.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz (skylake_avx512), Python 2.7.5
See https://gist.github.com/fd4e55089487233bf57b92a1126822b6 for a full test report.

[branfosj]

@lexming

== 2021-08-16 18:41:57,201 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd " R CMD INSTALL /tmp/4061310.master01.hydra.brussel.vsc/RbundleBioconductor/3.13/foss-2021a-R-4.1.0/ccmap/ccmap   --library=/tmp/vsc10009/ebinstall/13044/software/R-bundle-Bioconductor/3.13-foss-2021a-R-4.1.0/ --no-clean-on-error " exited with exit code 1 and output:
ERROR: dependency 'xgboost' is not available for package 'ccmap'

xgboost was added to the R easyconfig in #13284

[smoors]

@branfosj thanks, @lexming is my colleague ;)

[smoors]

Test report by @smoors
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node354.hydra.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz (skylake_avx512), Python 2.7.5
See https://gist.github.com/61abd715942e521e7a152f49f768b81a for a full test report.

[smoors]

lgtm

requested changes addressed

[smoors]

Going in, thanks @branfosj!