Contrib r 3.1.1 intel 2014b #956

hajgato · 2014-07-08T09:50:16Z

And dependencies (upgraded to latest version) with intel2014b.
Easyblock updates are necessary for generic/rpackage.py and r/rmpi.py
easybuilders/easybuild-easyblocks#435

hpcugentbot · 2014-07-08T09:50:18Z

Automatic reply from Jenkins: Can I test this?

hajgato · 2014-07-08T10:04:30Z

I think I mixed something. Files
easybuild/easyconfigs/a/Armadillo/Armadillo-4.300.8-ictce-5.5.0-Python-2.7.5.eb
easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb
easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb
should not be there.

wpoely86 · 2014-07-16T16:46:18Z

@hajgato delete them from this PR? Or close this PR and open a new one?

hajgato · 2014-07-22T11:43:18Z

Unwanted files are deleted

wpoely86 · 2014-07-28T09:41:28Z

ok to test

wpoely86 · 2014-07-28T09:45:51Z

easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb

+toolchainopts = {'pic': True}
+
+sources = ['readline-%(version)s.tar.gz']
+source_urls = ['http://ftp.gnu.org/gnu/readline']


Use SOURCE_TAR_GZ and GNU_SOURCE here

a wait, I see the problem. Ignore this.

wpoely86 · 2014-07-29T08:49:19Z

Test report by @wpoely86
FAILED
Build succeeded for 4 out of 6
Linux debian 7.6, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/caeefec8f7f46a81796e for a full test report.

wpoely86 · 2014-07-29T09:05:06Z

Test report by @wpoely86
FAILED
Build succeeded for 5 out of 6
Linux debian 7.6, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/39907edb45dabb925fdb for a full test report.

wpoely86 · 2014-07-29T09:11:47Z

My test fails on a system libjpeg issue. Maybe add libjpeg to the dependencies?

hajgato · 2014-07-29T09:21:07Z

I am always wondering what should be in the dependecies. Should I define a system libjpeg dependency or a libjpeg via an easyconfig?

wpoely86 · 2014-07-29T09:24:52Z

Add libjpeg to the easyconfig dependencies. We only use system deps when there is a special reason.

wpoely86 · 2014-07-29T13:42:17Z

Test report by @wpoely86
FAILED
Build succeeded for 7 out of 8
Linux debian 7.6, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/2a1f7d3fed006eabea86 for a full test report.

wpoely86 · 2014-07-29T13:51:12Z

OK, this last one is actually successful. It fail because of a issue in libreadline on this build system (it's not linking to libtinfo that can be ignored.

boegel · 2014-08-01T08:48:11Z

I'd like to see the R easyconfig synced with the one in #908... @hajgato: did you just bump the version of R, or also the libraries?

hajgato · 2014-08-01T08:52:40Z

@boegel I updated all libraries to the newest the versions (on the date in the configfile, plus i added a bunch of libraries (what we use). I think this is an extension to #908, maybe some libraries a bit newer.

hajgato · 2014-08-01T08:53:43Z

Well the libraries were up-to date at 30 June 2014

boegel · 2014-08-01T08:57:38Z

@hajgato: ok, thanks for the info. In that case, I'll update #908 to sync up with this one.

hajgato · 2014-08-01T09:00:56Z

Well, this is the intel2014b toolchain, #908 is ictce 5.5.0 Plus I upgraded the dependencies.

boegel · 2014-08-01T09:27:26Z

@hajgato: we typically keep easyconfigs in sync across toolchains

hajgato · 2014-08-01T09:41:33Z

I was a rookie. I did not know about it. But I am afraid, I upgraded all the dependencies to the newest. :(

boegel · 2014-08-01T09:43:32Z

No problem, that's good, it shouldn't be too far of from the versions in my PR. I'll sync that with yours.

boegel · 2014-08-04T15:12:10Z

I suggest we bump this to v3.1.1 rather than trying to sync both PRs (which is quite painful, I tried).

See hajgato#4

hajgato · 2014-08-05T06:53:17Z

Makes sense.

bump version to v3.1.1 + add a couple more extensions to sync with R v3.1.0 easyconfig

hajgato · 2014-08-05T07:19:46Z

Sorry guys for the mess with the extensions, I have learnt my lesson.

hajgato · 2014-08-05T08:10:37Z

@boegel mlogit needs maxLik as dependency. Order have to be changed.

boegel · 2014-08-05T08:21:47Z

@hajgato: hajgato#5

fix exts orderr + include optparse

boegel · 2014-08-05T08:43:05Z

Test report by @boegel
FAILED
Build succeeded for 6 out of 7
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/1da653dfd5d9da635755 for a full test report.

bump versions for bioconductor pkgs

add more R extensions in R v3.1.1 easyconfig

remove double permute

boegel · 2014-08-05T11:17:08Z

Test report by @boegel
FAILED
Build succeeded for 6 out of 7
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/a5fb47bc7658eb54e830 for a full test report.

boegel · 2014-08-05T11:21:26Z

easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb

+    ('clusterGeneration', '1.3.1', ext_options),
+    ('raster', '2.2-31', ext_options),
+    ('dismo', '0.9-3', ext_options),
+    ('gsl', '1.9-10', ext_options),


This R package has an external dependency on the GSL library, so it should be installed using a separate easyconfig file.

provide a separate easyconfig file for gsl package that depends on GSL

fix toolchain in easyconfig for gsl R package

hajgato · 2014-08-06T11:33:03Z

ERROR: dependency ‘gsl’ is not available for package ‘evmix’

hajgato · 2014-08-06T11:41:46Z

I separated the evmix package, I am thesting now the intel/2014b version

hajgato · 2014-08-06T12:31:16Z

ERROR: dependency ‘miscTools’ is not available for package ‘maxLik’
Reordered package order accordingly. Another test.

hajgato · 2014-08-06T13:27:41Z

@boegel I fixed the intel/2014b version, can you do the ictce one? (I do not know where are your files)

hajgato mentioned this pull request Jul 9, 2014

Python2/3 with intel2014b #962

Merged

wpoely86 reviewed Jul 28, 2014
View reviewed changes

wpoely86 mentioned this pull request Jul 29, 2014

R 3.1.0 with multithreaded support #952

Closed

Merge pull request #4 from boegel/contrib_R-3.1.0-intel-2014b

48f82ee

bump version to v3.1.1 + add a couple more extensions to sync with R v3.1.0 easyconfig

Merge pull request #5 from boegel/contrib_R-3.1.0-intel-2014b

64f3f5b

fix exts orderr + include optparse

boegel changed the title ~~Contrib r 3.1.0 intel 2014b~~ Contrib r 3.1.1 intel 2014b Aug 5, 2014

Balázs Hajgató added 3 commits August 5, 2014 11:10

Merge pull request #6 from boegel/contrib_R-3.1.0-intel-2014b

a3a7401

bump versions for bioconductor pkgs

Merge pull request #7 from boegel/contrib_R-3.1.0-intel-2014b

7bcb6f4

add more R extensions in R v3.1.1 easyconfig

Merge pull request #8 from boegel/contrib_R-3.1.0-intel-2014b

fb3e09b

remove double permute

boegel reviewed Aug 5, 2014
View reviewed changes

Balázs Hajgató added 2 commits August 5, 2014 13:50

Merge pull request #9 from boegel/contrib_R-3.1.0-intel-2014b

29e787b

provide a separate easyconfig file for gsl package that depends on GSL

Merge pull request #10 from boegel/contrib_R-3.1.0-intel-2014b

62d2455

fix toolchain in easyconfig for gsl R package

evmix separated, package order fixed

13ac2ff

JackPerdue mentioned this pull request Aug 12, 2014

R 3.1.1 with multithreaded support (was PR#952) #1022

Merged

boegel mentioned this pull request Sep 10, 2014

add easyconfigs for R v3.1.x #1077

Merged

boegel merged commit 13ac2ff into easybuilders:develop Sep 10, 2014

hajgato deleted the contrib_R-3.1.0-intel-2014b branch October 16, 2014 08:39

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Contrib r 3.1.1 intel 2014b #956

Contrib r 3.1.1 intel 2014b #956

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Contrib r 3.1.1 intel 2014b #956

Contrib r 3.1.1 intel 2014b #956

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