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Author SHA1 Message Date
Glenn Johnson
4850b9d4d1 Make install comment consistent with actual call. 2016-06-16 23:08:55 -05:00
Glenn Johnson
7da405e630 Add validator for bioconductor packages 
This commit adds a validator function to make sure the versions of R and
bioconductor are in sync.
 2016-06-16 23:08:55 -05:00
Glenn Johnson
7213b12324 Tweak how R packages are built. 
Add bzip2 as a dependency to base R.

Switch from installing the R packages from tar files to installing from
the extracted directory. This is more in line with a standard install
and also allows installing from VCS.

Use the Bioconductor version for BiocGenerics and future Bioconductor
packages. Suffix the package with 'bioc-$version' to indicate which
Bioconductor release the package is a part of. This is actually more
important than the actual version attached to individual packages
although those are subject to change within the Bioconductor branch.
 2016-06-16 23:08:55 -05:00
Glenn Johnson
0e64c25ffc Fix flake8 errors 
Use Bioconductor provided Short URL for homepage in BiocGenerics.
Wrap description text for utf variant in pcre.
 2016-06-16 23:08:54 -05:00
Glenn Johnson
37dc13edaf Update version of BiocGenerics 
The BioConductor repositories only keep the most recent version so this
has to be bumped.
 2016-06-16 23:08:54 -05:00
Glenn Johnson
8704a4ed35 Use configure_args rather than options 
Replaced 'options' with 'configure_args'. That seems like a better name
and is consistent with the packaging guide.
 2016-06-16 23:08:54 -05:00
Glenn Johnson
fe256870b4 Add variant for UTF support to pcre 
This will build PCRE with UTF support by default. That seems to be
reasonable for most environments.
 2016-06-16 23:08:54 -05:00
Glenn Johnson
cb3505769b Clean up R extensions 
Run the existing R extension packages through autopep8 to clean up.
 2016-06-16 23:07:13 -05:00
Glenn Johnson
6649f9edc2 Add version 3.3.0 of R 
This commit adds the 3.3.0 version of R and adds dependencies on curl
and pcre.
 2016-06-16 23:07:13 -05:00
Glenn Johnson
64acbbfcf0 Clean up R package files 
- remove unused imports
- apply pep8
- reformat text strings
 2016-06-16 23:07:13 -05:00
Mario Melara
df84fe0b58 Added init_config parameter so we don't initialize the config when user runs spack compiler add. Should ONLY add what user specifies. Find compilers takes in paths parameter. 2016-06-16 18:10:38 -07:00
Todd Gamblin
f351e011d1 Merge pull request #1068 from epfl-scitas/fixes/flake8_no_f405 
Flake8: ignore F405
 2016-06-16 17:13:01 -07:00
Todd Gamblin
9ee6cbfb40 Merge pull request #944 from adamjstewart/features/bertini 
Add bertini package
 2016-06-16 16:57:50 -07:00
Todd Gamblin
344280154a Merge pull request #962 from adamjstewart/features/hpl 
Add HPL benchmark package
 2016-06-16 16:57:24 -07:00
Todd Gamblin
005827ab23 Replace 2.6-incompatible skipIf with a conditional. 
- skipIf doesn't work with Python 2.6.
 2016-06-16 12:12:29 -07:00
Todd Gamblin
f60ae61652 remove dead code, cleanup. 2016-06-16 10:44:15 -07:00
Todd Gamblin
8867adf942 simplify instance check. 2016-06-16 10:43:36 -07:00
Todd Gamblin
c7dfa1699a rename Mac OS X to macos 2016-06-16 10:43:12 -07:00
alalazo
a5aa159d9d flake8: ignore F405 2016-06-16 19:23:16 +02:00
Mario Melara
6b03770602 Added str method to mac_osx so that whenever we try to access darwins different operating systems we can grab the name correctly. This avoids having to worry whether we have a version attached to it or not. 2016-06-16 09:44:37 -07:00
Todd Gamblin
88b73bacdb Merge branch 'features/newarch' into develop 
Conflicts:
	lib/spack/spack/config.py
	var/spack/repos/builtin/packages/lua/package.py
 2016-06-16 03:03:26 -07:00
Todd Gamblin
17b868381f Fixes #460: Do not show variants by default in spack find. 
This does two things:

1. By default `spack find` no longer shows variants.  You have to
   supply `-v` to get that

2. This improves the `colify` implementation so that it no longer pads
   the rightmost column.  This avoids the issue where if one spec was
   too long in the output, *all* specs would have space padding added
   to that width, and it would look like the output of `spack find`
   was double spaced.  This no longer happens -- the one bad line
   wraps around and the other lines are now single-spaced when you use
   `-v` with boost.
 2016-06-16 02:55:33 -07:00
alalazo
a1cbb73f8b qa : fixed flake8 issues 2016-06-16 11:24:18 +02:00
alalazo
8d9ffcf565 espresso : updated to 5.4.0, added Parallel=False 2016-06-16 11:22:26 +02:00
Todd Gamblin
88b671f8b1 Just call old os "unknown" 2016-06-16 02:06:19 -07:00
Todd Gamblin
76dfaa71a7 fix up packages for new architecture. 2016-06-16 01:47:20 -07:00
Todd Gamblin
40d25d9062 Add libxcb dependencies. Fix up packages to get py-basemap and stat to build. 2016-06-16 00:56:53 -07:00
Todd Gamblin
f3d6818d5c be more tolerant when parsing new specs. 2016-06-16 00:55:39 -07:00
Todd Gamblin
c90cc465f5 Add __contains__ to arch to satsify old packages. 2016-06-16 00:54:59 -07:00
Gregory L. Lee
d4df4375d5 removed unused import per flake8 report 2016-06-15 20:32:08 -07:00
Gregory L. Lee
1724ff5658 do not create shebang.bak file 2016-06-15 20:21:02 -07:00
Gregory Becker
3fcd54203c two minor fixes 2016-06-15 16:44:38 -07:00
Gregory Becker
2fc9ac4036 Two minor fixes 2016-06-15 16:39:39 -07:00
Erik Schnetter
a7ab064a9e Update OpenMPI to 1.10.3 2016-06-15 18:05:23 -04:00
Adam J. Stewart
ea80c8d3c3 Ignore E501 for depends_on and extends 2016-06-15 14:38:53 -05:00
Massimiliano Culpo
daa46105a7 mpich based providers : shortened filter_compilers 2016-06-15 21:37:12 +02:00
Adam J. Stewart
44e188f111 Remove MPI support, fix INCLUDE filters 2016-06-15 14:17:30 -05:00
Adam J. Stewart
7b97ea248a More template filtering 2016-06-15 14:17:29 -05:00
Adam J. Stewart
9cf1257be4 Filter compilers 2016-06-15 14:17:29 -05:00
Adam J. Stewart
deb4f919cf Psi4 tweaks 2016-06-15 14:17:29 -05:00
Adam J. Stewart
9d99042fed Add Psi4 package 2016-06-15 14:17:29 -05:00
Ben Boeckel
716f12dd58 reindex: preserve 'explicit' flags 
Look up in the old database whether the spec was explicit or not and
preserve it into the new database.

Fixes #1050.
 2016-06-15 12:48:40 -04:00
Denis Davydov
0e04e65ae0 trilinos: specify superlu-dist version dependency 2016-06-15 18:44:59 +02:00
Denis Davydov
5fe531050c flake8 fixes for dealii 2016-06-15 18:33:34 +02:00
Denis Davydov
e76083205f flake8 fixes for slepc 2016-06-15 18:33:08 +02:00
Denis Davydov
6390acc660 flake8 fixes for petsc 2016-06-15 18:32:42 +02:00
Denis Davydov
6d714e4425 flake8 fixes for superlu-dist 2016-06-15 18:31:39 +02:00
Denis Davydov
3d3a26cd9a flake8 fixes for filesystem.py 2016-06-15 18:31:10 +02:00
Ben Boeckel
36decbfa69 tty: do not break long words 
These "words" tend to be file paths which are best left unbroken.

Fixes #1057.
 2016-06-15 12:22:35 -04:00
Denis Davydov
d0d83cfe1e slepc: build by default with Arpack 2016-06-15 18:21:13 +02:00