add easyconfigs for pplacer and OCaml deps (REVIEW) #1056

boegel · 2014-09-03T11:21:25Z

@pforai: this is one of the dependencies for QIIME...

depends on ~~easybuilders/easybuild-easyblocks#467~~

This reverts commit 42760da.

boegel · 2014-09-05T08:02:18Z

Test report by @boegel
FAILED
Build succeeded for 10 out of 23
Linux RHEL 6.3, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/7f8a1a6480a3e28f869f for a full test report.

boegel · 2014-09-05T14:26:46Z

Test report by @boegel
FAILED
Build succeeded for 1 out of 14
Linux RHEL 6.3, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/e9418cede5c56581926e for a full test report.

boegel · 2014-09-05T15:27:20Z

Test report by @boegel
FAILED
Build succeeded for 13 out of 14
Linux RHEL 6.3, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/c7e9e0c9784c94d1ad1e for a full test report.

boegel · 2014-09-05T15:48:16Z

Test report by @boegel
FAILED
Build succeeded for 12 out of 14
Linux RHEL 6.3, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/bdb6c7b24f17c27549f0 for a full test report.

boegel · 2014-09-10T22:34:57Z

Test report by @boegel
FAILED
Build succeeded for 12 out of 14
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/3b49075fb553bd7ffb51 for a full test report.

hpcugentbot · 2014-10-10T14:53:47Z

Test PASSed.

boegel · 2014-10-10T15:07:41Z

@wpoely86: please review?

boegel · 2014-10-10T15:18:29Z

Test report by @boegel
FAILED
Build succeeded for 4 out of 14
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/928ad24181fade4bde0f for a full test report.

This reverts commit 9f73f3d.

hpcugentbot · 2014-10-10T15:26:40Z

Test PASSed.

boegel · 2014-10-10T15:41:56Z

Test report by @boegel
SUCCESS
Build succeeded for 14 out of 14
Linux SL 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/e2340da72984fe54b042 for a full test report.

boegel · 2014-10-10T15:51:32Z

Works fine on top of easybuilders/easybuild-easyblocks#467, awaiting review before merging it in...

boegel · 2014-10-11T07:52:45Z

@wpoely86: please review

wpoely86 · 2014-10-11T12:27:00Z

Looks fine but shouldn't we make a OCaml package easyblock? Now there a lot of duplicate code in all those easyconfigs?

boegel · 2014-10-13T07:42:27Z

@wpoely86: good suggestion... I'll look into it before merging this in.

fgeorgatos · 2014-12-16T13:41:08Z

fyi. I gave a visual review on this one and it looks good (but not the easyblock really).
except for verifying the builddep of ocaml, there is no other comment, looks useful PR.

fgeorgatos · 2015-04-05T16:54:52Z

easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb

+patches = ['OCaml-%(version)s_icc-fixes.patch']
+
+builddependencies = [('Autoconf', '2.69')]
+dependencies = [('ncurses', '5.9')]


I come to realize that if ncurses is there, I bet libreadline should also be. ditto for goolf.
ldd will prove the case

seems not:

-bash-4.1$ ldd /gpfs/scratch/projects/project_gpilot/vsc40023/software/OCaml/4.01.0-ictce-5.5.0/bin/* | grep ncurses libncurses.so.5 => /gpfs/scratch/projects/project_gpilot/vsc40023/software/ncurses/5.9-ictce-5.5.0/lib/libncurses.so.5 (0x00002aaaab152000) libncurses.so.5 => /gpfs/scratch/projects/project_gpilot/vsc40023/software/ncurses/5.9-ictce-5.5.0/lib/libncurses.so.5 (0x00002aaaab152000) -bash-4.1$ ldd /gpfs/scratch/projects/project_gpilot/vsc40023/software/OCaml/4.01.0-ictce-5.5.0/bin/* | grep readline -bash-4.1$

hpcugentbot · 2015-05-19T21:07:14Z

Refer to this link for build results (access rights to CI server needed):
https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/3029/
Test FAILed.

rjeschmi · 2015-05-20T02:45:18Z

There's an interesting mix here. Are some of these actually extensions of OCaml?

I haven't got my test space working yet for this yet, but I'll try to build tomorrow

hpcugentbot · 2016-02-21T15:22:04Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/6444/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

hpcugentbot · 2016-02-21T15:25:02Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/6445/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

hpcugentbot · 2016-02-21T16:34:17Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/6446/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

hpcugentbot · 2016-02-21T16:42:42Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/6447/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

boegel · 2016-02-21T17:32:35Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/6f7e12fd2660e1759dcb for a full test report.

boegel · 2016-02-21T17:43:44Z

easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha16-ictce-5.5.0-OCaml-4.01.0.eb

@@ -0,0 +1,51 @@
+easyblock = 'MakeCp'


needs to be changed to OCamlPackage

well, maybe not... the build procedure here is quite different

hpcugentbot · 2016-02-21T18:09:32Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/6453/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

hpcugentbot · 2016-02-22T19:38:18Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/6499/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

boegel · 2016-02-22T20:48:19Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/987fb8bb7d46a9391501 for a full test report.

boegel · 2016-02-22T21:47:41Z

I think this is good to go (finally!).

Final review, anyone? @wpoely86?

wpoely86 · 2016-02-23T09:15:33Z

easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb

+    'https://github.com/ocaml/opam/releases/download/%s' % opam_ver,
+]
+sources = [
+    'ocaml-%(version)s.tar.gz',


NAMELOWER_TAR_GZ?

no, but SOURCELOWER_TAR_GZ would work ;)

hpcugentbot · 2016-02-23T11:15:15Z

Easyconfigs unit test suite FAILed.

See https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/6513/console for more details.

Please fix the reported issues by pushing additional commits to the branch corresponding with this pull request; contact @boegel if you're not sure what to do.

boegel · 2016-02-23T21:15:01Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
Linux SL 6.7, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/5e1ef8411e2473b56a1b for a full test report.

boegel · 2016-02-23T21:18:57Z

Tested on top of easybuilders/easybuild-easyblocks#835, thanks for the feedback everyone!

boegel · 2016-02-24T06:43:18Z

Jenkins: test this please

hpcugentbot · 2016-02-24T06:56:30Z

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/6555/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

add easyconfigs for pplacer and OCaml deps (REVIEW)

add easyconfigs for pplacer and OCaml deps

6d5ab1a

This was referenced Sep 3, 2014

add easyblock for OCaml with support for extensions + generic OCamlPackage easyblock easybuilders/easybuild-easyblocks#467

Merged

add easyconfigs for QIIME and dependencies #1057

Closed

boegel added 4 commits September 4, 2014 09:08

ad missing patch file for csv

fc5be44

add zlib dependency for pplacer

42760da

Revert "add zlib dependency for pplacer"

9c13932

This reverts commit 42760da.

fix location of findlib.conf

8172280

get rid of unnecessary patch for OCaml with ictce

9f73f3d

Revert "get rid of unnecessary patch for OCaml with ictce"

53128ed

This reverts commit 9f73f3d.

boegel mentioned this pull request Oct 10, 2014

Unison #1128

Closed

fgeorgatos reviewed Apr 5, 2015
View reviewed changes

boegel added 2 commits May 19, 2015 15:14

Merge branch 'develop' into ocaml_pplacer

4c7d79d

include extensions in OCaml easyconfigs

b9f6e36

boegel added 2 commits February 21, 2016 15:54

Merge branch 'develop' into ocaml_pplacer

137ebfd

stick to libreadline 6.2

b825580

boegel added 2 commits February 21, 2016 17:21

sync up OCaml 4.01.0 easyconfigs

bb8088a

fix source URLs for OCaml

71836c9

boegel reviewed Feb 21, 2016
View reviewed changes

add comment in patch file

7536aa2

fix output of 'pplacer --version'

287331b

boegel changed the title ~~add easyconfigs for pplacer and OCaml deps (WIP)~~ add easyconfigs for pplacer and OCaml deps (REVIEW) Feb 22, 2016

wpoely86 reviewed Feb 23, 2016
View reviewed changes

boegel added 2 commits February 23, 2016 11:14

fix remark

afdf8a5

use pplacer easyblock

8cb4757

boegel mentioned this pull request Feb 23, 2016

add easyblock for pplacer easybuilders/easybuild-easyblocks#835

Merged

boegel added a commit that referenced this pull request Feb 24, 2016

Merge pull request #1056 from boegel/ocaml_pplacer

9d56e58

add easyconfigs for pplacer and OCaml deps (REVIEW)

boegel merged commit 9d56e58 into easybuilders:develop Feb 24, 2016

boegel deleted the ocaml_pplacer branch February 24, 2016 07:47

add easyconfigs for pplacer and OCaml deps (REVIEW) #1056

add easyconfigs for pplacer and OCaml deps (REVIEW) #1056

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