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Author SHA1 Message Date
becker33
91004158c6 Merge pull request #1243 from davydden/pkg/atlas_urls 
atlas: fix urls and shared libs
 2016-08-02 09:59:05 -07:00
becker33
3f26bbc8b3 Merge pull request #864 from davydden/kdiff3 
kdiff3: initial version of the package
 2016-08-02 09:35:00 -07:00
becker33
a3322fab0a Merge pull request #1360 from glennpj/pysetuptoolsdep 
Add py-setuptools dependencies to packages
 2016-08-02 09:33:40 -07:00
becker33
21158195fb Merge pull request #1354 from paulhopkins/bugfix/preferred_variants_do_not_recognise_-variant 
Bugfix/preferred variants do not recognise  -variant
 2016-08-02 09:15:06 -07:00
George Hartzell
74a181febc Remove local copy of cpanm installer 
This is handled as a resource in the package now.
 2016-08-02 12:13:24 -04:00
George Hartzell
4c8672ed1f Add previous versions back into package 
Following the advice of @glennpj, added the old versions back into the
packages.

I can install the current packages and the previous packages.
 2016-08-02 11:45:16 -04:00
George Hartzell
c77425bb22 Remove useless def unpack 
Before I learned that I was stumbling over a real but (#1308), I thought
I needed to arrange for the fetcher to skip the unpack step.

This commit removes the useful `def unpack`.
 2016-08-02 11:32:19 -04:00
George Hartzell
a6605d842b Flake8 cleanup. 2016-08-02 11:25:03 -04:00
George Hartzell
f2f5f6c279 Touch up variant comment 2016-08-02 11:18:50 -04:00
George Hartzell
c994565c62 Use "resource" machinery to manage cpanm tarball 
Use the resource machinery to fetch/cache/unpack/... the App::cpanminus
tarball.

- this hardcodes the version, I can't figure out how to use a variant to
  hold/set the value and access it in the resource().
- change up the install to use the `with working_dir()` meme.
 2016-08-02 11:16:46 -04:00
George Hartzell
1b9becc541 Add the std spack header to perl/package.py 
Stole the example header from antlr/package.py, included it at the top
of perl/package.py.
 2016-08-02 11:16:46 -04:00
George Hartzell
08ff7b65af Make running perl's tests conditional 
Make running perl's tests conditional, one must now specify the
`--run-tests` flag to the `spack install` command in order to run the
tests.

On one system (8 core, 16GB Digital Ocean Droplet), installing without
tests takes 3 minutes, with tests takes 16 minutes.
 2016-08-02 11:16:46 -04:00
George Hartzell
4d72e0fb9d Make the cpanm version a variant 
Rather than hard-coding the verison of `cpanm` that's [optionally]
installed into the core, make it a variant with a default value of
'1.7042'.

Also discovered that `prefix + 'bin'` is the same as `prefix.bin`, so
embetter that bit of code.
 2016-08-02 11:16:46 -04:00
George Hartzell
a5a4525bed Add perl package 
Add perl package, based on [work by
justintoo](https://github.com/LLNL/spack/pull/105).  He had too many
things pulled into that pull request, this just adds a perl package.

Support the current releases on the past three minor branches.

Run perl's tests before installing.

Install cpanm into the core (makes building on top of this perl *much*
simpler).  Controlled by a variant.
 2016-08-02 11:16:46 -04:00
George Hartzell
949621eb7f Add package for texlive 2016-08-02 11:15:42 -04:00
George Hartzell
857a03c127 Ack should depends_on('perl') 
Add a depends_on('perl') and rewrite the script's `#!` line to refer to
that Perl's `perl` executable.
 2016-08-02 11:11:05 -04:00
George Hartzell
114da813a3 Remove unnecessary imports. 
Now that it's sporting a cleaner install method, these imports are
unnecessary.
 2016-08-02 11:11:05 -04:00
George Hartzell
bf467c5df3 Remove override of unpack(self) 
I cargo culted that from my *nextflow* package.  I [thought I] needed it
to work around Spack trying to use tar to unpack something that was
neither a tar ball nor unpackable.

This package works fine without it.  In retrospect, the error that I was
seeing in the *nextflow* package was probably this problem #1308.
 2016-08-02 11:11:05 -04:00
George Hartzell
6c3623422f Use cleaner mech to install script 
Use @adamjstewart's nicer bit of python code in the
install method.
 2016-08-02 11:11:05 -04:00
George Hartzell
63121a0c49 Add package for ack 
Add a package for [ack](http://beyondgrep.com/install/).  Simply install
the fatpacked script.

It uses '#!/usr/bin/env perl' and it very much not choosy about what
perl it needs.  For now just trust that there's one available, perhaps
someday we can/should uncomment the depends_on('perl').

Follows the methodolgy I used in nextflow.  Has the same
uninstall/install problem that nextflow has, there is an issue in
progress for that: https://github.com/LLNL/spack/issues/1308.

Tested on CentOS7.
 2016-08-02 11:11:05 -04:00
George Hartzell
12d1263980 Update several R packages (r-shiny prereqs) 
r-jsonlite 0.0.21 -> 1.0
r-mime     0.4    -> 0.5
rcpp       0.12.5 -> 0.12.6

CRAN is funny.  The older versions of these packages are still available
in package specific directories but the current version is not there, so
I don't see any way to make the older versions work.
 2016-08-02 11:10:41 -04:00
George Hartzell
6f332c7e4c Fix whitespace, make flake8 happ{y,ier}. 2016-08-02 11:10:12 -04:00
George Hartzell
bfcec69630 Add standard header, use spack helpers 
Added the standard header (stolen from R).

Touched up the install to use set_executable rather than doing it
myself.
 2016-08-02 11:10:12 -04:00
George Hartzell
4373a2b629 First cut package for nextflow, has issues 
This is my first cut at a package to support nextflow.  It's also my
first package.  It works, but has issues.  I'm going to submit a pull
request and get some coaching on how to deal with it.

One issue particular: if I install, then uninstall, then try to install
again (which uses the cached copy of the "distribution file"), it
explodes.
 2016-08-02 11:10:12 -04:00
Glenn Johnson
a57d94af03 Fix flake8 issues. 2016-08-02 09:53:57 -05:00
Denis Davydov
a1703bf70d kdiff3: add license block 2016-08-02 16:37:14 +02:00
Gilles Fourestey
dea7bbb4a0 added plumed 
* plumed : first version
* plumed : added dependencies and docs
 2016-08-02 15:06:46 +02:00
Denis Davydov
565bd5f51e atlas: revert to lapack 3.5.0 2016-08-02 13:52:32 +02:00
Denis Davydov
bef7e2645a atlas: flake8 fixes 2016-08-02 13:52:32 +02:00
Denis Davydov
f6a4a6b00f atlas: add install_test 2016-08-02 13:52:32 +02:00
Denis Davydov
0c0b37800d atlas: set (blas|lapack)_shared_lib 2016-08-02 13:52:32 +02:00
Denis Davydov
4ecf481337 atlas: fix shared libs; set compilers 2016-08-02 13:52:32 +02:00
Denis Davydov
6f7e12d49b atlas: fix urls and use lapack 3.6.0 2016-08-02 13:52:32 +02:00
Denis Davydov
0aa513ad70 libxau: mark pkg-config as build-type dependency 2016-08-02 13:50:46 +02:00
Denis Davydov
450c750214 kdiff3: initial version of the package 2016-08-02 13:49:40 +02:00
Denis Davydov
a4e59c2758 libxau: add missing dependency 2016-08-02 13:49:40 +02:00
Kelly (KT) Thompson
9433e84776 Formatting changes for flake8. 2016-08-01 22:54:51 -06:00
Kelly (KT) Thompson
17f0eb5148 Provide correct download urls and additional dependencies. 2016-08-01 22:10:54 -06:00
ba11f19efc Merge remote-tracking branch 'upstream/develop' into gktplus3-deps 2016-08-01 20:50:28 -06:00
becker33
b892cebe8a Merge pull request #1343 from glennpj/r_unfilter 
R extension dependencies with compiler wrapper
 2016-08-01 13:51:13 -07:00
becker33
e861e35acf Merge pull request #1234 from mwilliammyers/package-opencv 
Update opencv package
 2016-08-01 13:44:31 -07:00
becker33
1847aa035d Merge pull request #1348 from glennpj/rcurl 
r-curl update and changed remote archive
 2016-08-01 13:38:38 -07:00
becker33
94238eebfa Merge pull request #1381 from davydden/pkg/mkl_linux 
MKL linux fixes
 2016-08-01 13:36:10 -07:00
becker33
dc9fcea989 Merge pull request #1365 from hartzell/feature/add-package-for-tree 
Add package for tree
 2016-08-01 13:21:09 -07:00
becker33
15514792d5 Merge pull request #1374 from hartzell/bug/fix-jdk-import-of-distutils 
Bug: fix jdk package's use of distutils
 2016-08-01 13:20:44 -07:00
becker33
851bc506e4 Merge pull request #1367 from adamjstewart/features/pgi 
Add latest version of PGI
 2016-08-01 13:07:35 -07:00
becker33
932300256c Merge pull request #1413 from mdevlin1/fixes/libxsmm 
Fixed libxsmm package
 2016-08-01 13:06:05 -07:00
becker33
6361f5c2d4 Merge pull request #1359 from sknigh/libhio 
added libhio package
 2016-08-01 13:05:29 -07:00
Mitchell Devlin
2d51ea5da4 fixed libxsmm makefile filter 2016-08-01 14:38:16 -05:00
Adam J. Stewart
fed7ba1dab Add latest version of PGI 2016-08-01 13:42:00 -05:00
Adam J. Stewart
ab885a5397 Allow git to depend on gettext now that it works 2016-08-01 13:35:22 -05:00
Adam J. Stewart
4014a29d2b Use proper deptype so that spack activate works 2016-08-01 13:35:22 -05:00
Adam J. Stewart
f5aed63b0b pkg-config should be a build dependency only 2016-08-01 13:35:22 -05:00
Adam J. Stewart
5cac0a528c Fix undefined symbols by building shared libraries 2016-08-01 13:35:22 -05:00
Adam J. Stewart
bdb64c2e39 Tell MEEP where to find libctl 2016-08-01 13:35:22 -05:00
Adam J. Stewart
0903ae0599 Final fixes to get libctl working 2016-08-01 13:35:22 -05:00
Adam J. Stewart
1e3a5d4e26 Final fixes to get guile to build 2016-08-01 13:35:21 -05:00
Adam J. Stewart
6db99a4fe7 Rename gc => bdw-gc, fix libunistring bug 2016-08-01 13:35:21 -05:00
Adam J. Stewart
5b1a882fc2 Update meep's url_for_version 2016-08-01 13:35:21 -05:00
Adam J. Stewart
a2578c21e4 Supply flags to bdist 2016-08-01 13:35:21 -05:00
Adam J. Stewart
8d0758fc4c Allow py-meep to link properly 2016-08-01 13:35:21 -05:00
Adam J. Stewart
880cbb2217 Better testing for MEEP 2016-08-01 13:35:21 -05:00
Adam J. Stewart
3b4820f290 Patch pkg-config and update installs for various packages 2016-08-01 13:35:21 -05:00
Adam J. Stewart
9e05fdf4a1 Bug fixes 2016-08-01 13:35:20 -05:00
Adam J. Stewart
7e53f4328f Add py-meep package and dependencies 2016-08-01 13:35:20 -05:00
George Hartzell
7d303afd64 Address flake8 issue 2016-08-01 13:42:55 -04:00
George Hartzell
1552ed943a Add package for cask 
Add a package for cask, the emacs project/dependency management tool.

Based on [Homebrew's formula][brew].

[brew]: https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb
 2016-08-01 13:41:28 -04:00
George Hartzell
31b7580b76 Fix jdk package's use of distutils 
See issue #1364.  @citibeth's fix works fine.
 2016-08-01 13:33:27 -04:00
becker33
cc3fc2ba4c Merge pull request #1322 from mdevlin1/feature/libxsmm 
Add libxsmm package
 2016-08-01 09:56:09 -07:00
Paul Hopkins
cca240c8f9 Add concretize_preferences tests 2016-08-01 16:18:11 +01:00
alalazo
ec09dfe5d1 cp2k : added package 2016-08-01 10:41:33 +02:00
Todd Gamblin
fbbb82259a Merge pull request #1407 from glennpj/r-ncdf4 
New package - r-ncdf4
 2016-07-31 22:15:52 -07:00
Todd Gamblin
ea11aab71f Merge pull request #1406 from glennpj/r-np 
New package - r-np
 2016-07-31 22:15:37 -07:00
Todd Gamblin
2042c94a6c Merge pull request #1405 from glennpj/r-survey 
New package - r-survey
 2016-07-31 22:15:09 -07:00
Todd Gamblin
64be8a80b2 Merge pull request #1404 from glennpj/r-tarifx 
New package - r-tarifx
 2016-07-31 22:14:56 -07:00
Todd Gamblin
7185fe2876 Merge pull request #1403 from glennpj/r-e1071 
New package - r-e1071
 2016-07-31 22:14:40 -07:00
Todd Gamblin
0724eba935 Merge pull request #1402 from glennpj/r-plotrix 
New package - r-plotrix
 2016-07-31 22:14:25 -07:00
Todd Gamblin
441bb83682 Merge pull request #1401 from glennpj/r-gdata 
New package - r-gdata
 2016-07-31 22:13:50 -07:00
Todd Gamblin
2cffc90284 Merge pull request #1400 from glennpj/r-roxygen2 
New package - r-roxygen2
 2016-07-31 22:13:16 -07:00
Todd Gamblin
68cedd2599 Merge pull request #1399 from glennpj/r-testthat 
New package - r-testthat
 2016-07-31 22:12:06 -07:00
Todd Gamblin
d00fd06095 Merge pull request #1398 from glennpj/r-xml 
New package - r-xml
 2016-07-31 22:11:38 -07:00
Glenn Johnson
8815f0a0b5 New package - r-ncdf4 
Interface to Unidata netCDF (version 4 or earlier) format data files.
 2016-07-31 17:12:29 -05:00
Glenn Johnson
bfd03db12a New package - r-np 
Nonparametric kernel smoothing methods for mixed data types.
 2016-07-31 16:18:55 -05:00
Glenn Johnson
f14eb07dc1 New package - r-survey 
Analysis of complex survey samples.
 2016-07-31 15:50:19 -05:00
Glenn Johnson
a9cc6a7d08 New package - r-tarifx 
A collection of various utility and convenience functions.
 2016-07-31 15:39:09 -05:00
Glenn Johnson
be2f2e42db New package - r-e1071 
Misc functions of the Department of Statistics, Probability Theory Group
(Formerly: E1071), TU Wien.
 2016-07-31 15:26:13 -05:00
Glenn Johnson
05e5276aec New package - r-plotrix 
Various plotting functions.
 2016-07-31 15:15:55 -05:00
Glenn Johnson
dbf799bbf9 New package - r-gdata 
Data manipulation tools.
 2016-07-31 15:07:40 -05:00
Glenn Johnson
f39e570f36 New package - r-roxygen2 
In-source documentation for R.
 2016-07-31 14:52:16 -05:00
Glenn Johnson
58a6039c0a New package - r-testthat 
A unit testing system for R.
 2016-07-31 14:40:46 -05:00
Glenn Johnson
0662b953f0 New package - r-xml 
Tools for parsing and generating XML within R and S-Plus.
 2016-07-31 14:25:17 -05:00
Glenn Johnson
1b04b8be01 New package - r-datatable 
Extension of Data.frame
 2016-07-31 14:11:04 -05:00
Todd Gamblin
173a16b38a Merge pull request #1396 from glennpj/r-quantmod 
New package - r-quantmod
 2016-07-30 20:15:53 -07:00
Todd Gamblin
68ba5377c1 Merge pull request #1395 from glennpj/r-ggmap 
New package - r-ggmap and dependencies
 2016-07-30 20:14:57 -07:00
Todd Gamblin
253507c0c3 Merge pull request #1394 from glennpj/r-maps 
New package - r-maps
 2016-07-30 20:14:27 -07:00
Todd Gamblin
7684652ce3 Merge pull request #1393 from glennpj/r-maptools 
New package - r-maptools
 2016-07-30 20:14:19 -07:00
Todd Gamblin
b12dc34ba7 Merge pull request #1391 from glennpj/r-caret 
New package - r-caret
 2016-07-30 20:14:09 -07:00
Todd Gamblin
9c31ee8a75 Merge pull request #1390 from glennpj/r-glmnet 
New package - r-glmnet
 2016-07-30 20:13:50 -07:00
Todd Gamblin
ae5ba2b110 Merge pull request #1389 from glennpj/r-vcd 
New package - r-vcd
 2016-07-30 20:13:05 -07:00
Todd Gamblin
13499f1655 Merge pull request #1388 from glennpj/r-multcomp 
New package - r-multcomp
 2016-07-30 20:12:51 -07:00