add easyconfigs for Circos + deps, including Perl update by boegel · Pull Request #780 · easybuilders/easybuild-easyconfigs

boegel · 2014-03-26T21:39:28Z

depends on easybuilders/easybuild-easyblocks#380 and easybuilders/easybuild-easyblocks#425 (sort of)

boegel · 2014-06-04T07:49:16Z

@wpoely86, @pescobar, @pforai: please review/test?
There's already a new version of Perl out, so we should leave this rotting...

boegel · 2014-06-04T08:22:22Z

Test report by @boegel
FAILED
Build succeeded for 5 out of 8
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/17c571e261cba5372633 for a full test report.

wpoely86 · 2014-06-04T20:33:35Z

why not use %(lowername) here ? Like below?

boegel · 2014-06-05T15:26:46Z

Test report by @boegel
FAILED
Build succeeded for 5 out of 8
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/53d26d70a8612d7eee1a for a full test report.

boegel · 2014-06-05T16:18:13Z

Test report by @boegel
SUCCESS
Build succeeded for 8 out of 8
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/2c62ed5a86003fa7b99c for a full test report.

boegel · 2014-06-05T16:52:23Z

@wpoely86: this seems to be ready now, tested on top of an enhanced easybuilders/easybuild-easyblocks#425

wpoely86 · 2014-06-05T18:12:51Z

Test report by @wpoely86
FAILED
Build succeeded for 4 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/de7d31830c91b0092920 for a full test report.

wpoely86 · 2014-06-05T20:07:45Z

@boegel I'm having issues downloading all the source files?

boegel · 2014-06-06T14:29:53Z

@wpoely86: can you retry, or try a manual download? EasyBuild can't control upstream issues...

wpoely86 · 2014-06-07T05:38:43Z

Test report by @wpoely86
FAILED
Build succeeded for 6 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/b32a18def5d532808b19 for a full test report.

wpoely86 · 2014-06-08T03:55:58Z

Test report by @wpoely86
FAILED
Build succeeded for 6 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/6e3f36c5b0e5adbbaa52 for a full test report.

wpoely86 · 2014-06-08T04:03:50Z

add 'http://search.cpan.org/CPAN/authors/id/E/ET/ETHER

no, drop that. I cannot find that old version of Moose. Why not update to 2.1209?

@wpoely86: it's available here (just google the file name) http://ftp.usa.openbsd.org/pub/OpenBSD/distfiles/

We could update all Perl modules listed here, but then it becomes a never-ending story... As it is now, the modules listed have the latest version available at the time when this was composed (i.e. shortly after Perl v5.18.2 was made available).

This again shows the need for an archiving solution of our own, since sources keep disappearing upstream...

An update of Perl and modules is available at #909 btw.

wpoely86 · 2014-06-09T04:20:18Z

Test report by @wpoely86
FAILED
Build succeeded for 6 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/11705bc08e91ee206fba for a full test report.

boegel · 2014-06-09T13:13:25Z

@wpoely86: I've removed the DB_File extension from the list, since it has an external dependency (cfr. #913); please retest?

wpoely86 · 2014-06-09T15:10:56Z

Test report by @wpoely86
FAILED
Build succeeded for 6 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/406b822062b0857ece5f for a full test report.

boegel · 2014-06-09T15:18:09Z

@wpoely86: OK, now BioPerl is failing... Makes sense, since it depends on DB_File. But, why didn't I run into this (I retested the build too)...

…eps)

boegel · 2014-06-09T20:22:15Z

@wpoely86: kicked out Bio::Perl, and created a dedicated easyconfig included in #913; it wasn't failing for me because our system Perl also provided DB_File...

boegel · 2014-06-11T06:33:36Z

@wpoely86: Still fails? Any idea what's going on?

wpoely86 · 2014-06-12T04:36:54Z

Test report by @wpoely86
FAILED
Build succeeded for 7 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/0c174d91e5aa3ca2f6e6 for a full test report.

wpoely86 · 2014-06-13T02:37:55Z

Test report by @wpoely86
FAILED
Build succeeded for 7 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/13f0957a92505ed1ba68 for a full test report.

wpoely86 · 2014-06-16T10:29:13Z

@boegel It's a test of gd that fails, but I don't see or know why?

boegel · 2014-07-07T12:16:58Z

@wpoely86: full debug log?

wpoely86 · 2014-07-08T12:27:29Z

Test report by @wpoely86
FAILED
Build succeeded for 7 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/dcd3a0fc48631a347429 for a full test report.

wpoely86 · 2014-07-08T12:34:40Z

@boegel this is where it goes wrong: https://gist.github.com/wpoely86/338c28baf21c33cdd723

boegel · 2014-07-08T15:01:06Z

@wpoely86: is there anything to see if you dive into the directory where the tests are run? Do you have libpng installed on this system? Maybe that's why it's failing (there's no direct libpng dep in the GD easyconfig, because I assume it's not required but maybe it is).

wpoely86 · 2014-07-09T10:09:32Z

Test report by @wpoely86
FAILED
Build succeeded for 7 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/24002c15e8d1d73f45d3 for a full test report.

wpoely86 · 2014-07-09T14:47:45Z

Test report by @wpoely86
SUCCESS
Build succeeded for 9 out of 9
Linux debian 7.2, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/dae7ecff830cb05eaa02 for a full test report.

wpoely86 · 2014-07-09T14:52:19Z

@boegel found it. I had libjpeg8-dev installed and this apparently only works with libjpeg62-dev ...

wpoely86 · 2014-07-09T14:52:29Z

And shouldn't it use Jasper?

boegel · 2014-09-09T15:31:36Z

@wpoely86: can you check whether adding JasPer as a dep for GD resolves the issue, even if you have libjpeg8-dev installed?

wpoely86 · 2014-09-09T15:33:40Z

libgd has a JasPer dep and GD has a libgd dep. So JasPer should be loaded?

boegel · 2014-09-09T15:44:30Z

yeah, but GD wants something that provides libjpeg.so, which JasPer doesn't... I'll look into switching from JasPer to libjpeg.

boegel · 2014-09-09T15:52:05Z

@wpoely86: please retest?

wpoely86 · 2014-09-09T16:21:55Z

Test report by @wpoely86
FAILED
Build succeeded for 15 out of 18
Linux debian 7.6, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/e886ea8dc15d9377e334 for a full test report.

boegel · 2014-09-09T16:31:05Z

Test report by @boegel
SUCCESS
Build succeeded for 12 out of 12
Linux RHEL 6.3, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/1418eaf58a066814916b for a full test report.

boegel · 2014-09-09T19:33:07Z

@wpoely86: I've fixed the download URLs for the Perl stuff as @hajgato did in #977, please try again?

boegel · 2014-09-09T20:03:40Z

Test report by @boegel
SUCCESS
Build succeeded for 11 out of 11
Linux RHEL 6.3, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/c0258962d1c0558a8fe2 for a full test report.

wpoely86 · 2014-09-10T09:01:34Z

Test report by @wpoely86
SUCCESS
Build succeeded for 18 out of 18
Linux debian 7.6, Intel(R) Xeon(R) CPU 5130 @ 2.00GHz, Python 2.7.3
See https://gist.github.com/ea1ea8735406a9ac1b52 for a full test report.

boegel · 2014-09-10T09:20:10Z

Hooray!

Thanks for the reviewing/testing @wpoely86.

Merging this in.

add easyconfigs for Circos + deps, including Perl update

fgeorgatos · 2014-11-26T22:27:37Z

Test report by @fgeorgatos
SUCCESS
Build succeeded for 11 out of 11
Linux debian 6.0.9, Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz, Python 2.6.6
See https://gist.github.com/0b10ba2732501d9adfbc for a full test report.

boegel added 6 commits March 26, 2014 16:44

add easyconfigs for Circos + deps, including Perl update

360a028

add Perl v5.18.2 specific patch file for tests

58dba12

disable broken test in Perl v5.18.2

d9c2a87

fix source URL for Class::Load Perl module

978b65d

add missing perl modules, fix source_urls

f9743fc

add missing patch file

8d751e4

boegel mentioned this pull request Jun 4, 2014

Jasper style fix #907

Merged

Merge branch 'develop' into circos

e95c97b

wpoely86 reviewed Jun 4, 2014
View reviewed changes

fix tiny remark

2f578c0

wpoely86 reviewed Jun 8, 2014
View reviewed changes

drop DB_File Perl extension since it has external dependencies

e9e1c5d

kick out Bio::Perl, since it depends on DB_File (which has external d…

d313d97

…eps)

boegel mentioned this pull request Jun 9, 2014

add easyconfig for DB_File Perl module + DB dep #913

Merged

switch from using JasPer to libjpeg-turbo

f4e346e

boegel added 2 commits September 9, 2014 17:52

add missing NASM easyconfig

f3849b6

fix conflict

6dd91ae

fix cpan source URLs

966ff29

boegel added a commit that referenced this pull request Sep 10, 2014

Merge pull request #780 from boegel/circos

bdc453c

add easyconfigs for Circos + deps, including Perl update

boegel merged commit bdc453c into easybuilders:develop Sep 10, 2014

boegel deleted the circos branch September 10, 2014 09:20

Conversation

boegel commented Mar 26, 2014

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