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add Repitools extension to R-bundle-Bioconductor 3.9 (and take into extension version in exts_filter)#9410

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verdurin merged 2 commits intoeasybuilders:developfrom
boegel:Bioc38_Repitools
Nov 29, 2019
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add Repitools extension to R-bundle-Bioconductor 3.9 (and take into extension version in exts_filter)#9410
verdurin merged 2 commits intoeasybuilders:developfrom
boegel:Bioc38_Repitools

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@boegel boegel commented Nov 29, 2019

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@boegel boegel added this to the 4.1.0 milestone Nov 29, 2019
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boegel commented Nov 29, 2019

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/97f17d11fe2a0b2de589e1b8c049a0cd for a full test report.

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boegel commented Nov 29, 2019

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2404.golett.os - Linux centos linux 7.7.1908, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/b1de3adb3aec15bc1753ec87ab5bb0dc for a full test report.

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boegel commented Nov 29, 2019

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node3169.skitty.os - Linux centos linux 7.7.1908, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/8204cbac3229e7e352648e58ccc967b7 for a full test report.

@verdurin verdurin changed the title add Repitools extension to R-bundle-Bioconductor 3.8 (and take into extension version in exts_filter) add Repitools extension to R-bundle-Bioconductor 3.9 (and take into extension version in exts_filter) Nov 29, 2019
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smoors commented Nov 29, 2019

Test report by @smoors
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node368.hydra.os - Linux centos linux 7.6.1810, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, Python 2.7.5
See https://gist.github.com/7a03df545e4c203b022ce12912e27fb5 for a full test report.

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Test report by @verdurin
FAILED
Build succeeded for 1 out of 2 (1 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.7.1908, Intel Xeon Processor (Skylake, IBRS), Python 2.7.5
See https://gist.github.com/d9065ac0a75c1eac29d337fc9992cc23 for a full test report.

smoors
smoors previously approved these changes Nov 29, 2019
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lgtm

…9 easyconfigs in case wrong extension version is found
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Here's my build failure:

== 2019-11-29 16:15:28,716 rpackage.py:225 DEBUG Installing R package MLInterfaces version 1.64.0.
== 2019-11-29 16:15:28,716 rpackage.py:152 DEBUG make_cmdline_cmd returns  R CMD INSTALL /eb/maint/sources/r/R-bundle-Bioconductor/extensions/MLInterfaces_1.64.0.tar.gz   --library=/eb/maint/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error
== 2019-11-29 16:15:28,716 run.py:200 DEBUG run_cmd: running cmd  R CMD INSTALL /eb/maint/sources/r/R-bundle-Bioconductor/extensions/MLInterfaces_1.64.0.tar.gz   --library=/eb/maint/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error  (in /tmp/eb-2acLcP/tmpBGdH44/easybuilders)
== 2019-11-29 16:15:28,716 run.py:219 INFO running cmd:  R CMD INSTALL /eb/maint/sources/r/R-bundle-Bioconductor/extensions/MLInterfaces_1.64.0.tar.gz   --library=/eb/maint/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error
== 2019-11-29 16:15:29,085 build_log.py:164 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd " R CMD INSTALL /eb/maint/sources/r/R-bundle-Bioconductor/extensions/MLInterfaces_1.64.0.tar.gz   --library=/eb/maint/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error " exited with exit code 1 and output:
ERROR: dependencies 'rda', 'threejs' are not available for package 'MLInterfaces'
 (at easybuild/tools/run.py:529 in parse_cmd_output)

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boegel commented Nov 29, 2019

@verdurin You need to add the missing extensions in your R installation using eb --force --skip, see #8881

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Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.7.1908, Intel Xeon Processor (Skylake, IBRS), Python 2.7.5
See https://gist.github.com/06a4527cfe8e6bfa0c6ba104c5447795 for a full test report.

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Looks fine.

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Going in, thanks @boegel!

@verdurin verdurin merged commit cfa0ffd into easybuilders:develop Nov 29, 2019
@boegel boegel deleted the Bioc38_Repitools branch November 29, 2019 18:19
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Building this gives me:
ERROR: dependency idr is not available for package ChIPpeakAnno
And, as far as I can see, idr is not part of the updated R/3.6.0 from #8881 either

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boegel commented Dec 3, 2019

@akesandgren idr is included in the R 3.6.0 easyconfigs in develop, was added via #9184

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Ok, this one didn't mention that one...

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4 participants