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Author SHA1 Message Date
Todd Gamblin
42ff1aaa75 Merge pull request #1064 from LLNL/bugfix/github-1043-script-backup 
do not create shebang.bak file
 2016-06-20 10:45:42 -07:00
Todd Gamblin
31bb47356f Merge pull request #1022 from glennpj/r-devtools 
new package: r-devtools
 2016-06-20 10:34:23 -07:00
Todd Gamblin
b3881701c5 Merge pull request #1021 from glennpj/packrat 
new package: r-packrat
 2016-06-20 10:33:55 -07:00
Todd Gamblin
0fbd2fe224 Merge pull request #1000 from glennpj/new_R 
Add version 3.3.0 of R and extensions
 2016-06-20 10:33:43 -07:00
Todd Gamblin
c09111bbef Merge pull request #1053 from davydden/pkg/dealii_suite_update 
update Petsc, Slepc, Trilinos, Superlu-dist and deal.II
 2016-06-20 10:32:52 -07:00
Todd Gamblin
59318f4705 Merge pull request #1081 from mathstuf/pkg-config-path 
modules.yaml: use the right envvar for pkg-config
 2016-06-20 10:32:03 -07:00
Todd Gamblin
8047edfb56 Merge pull request #1029 from adamjstewart/features/armadillo 
Add Armadillo and SuperLU packages
 2016-06-20 10:29:29 -07:00
Todd Gamblin
265b9bcb0f Merge pull request #1076 from JRWynneIII/ferret 
Added spec to build Ferret
 2016-06-20 10:28:42 -07:00
Todd Gamblin
12b9d6da10 Merge pull request #1083 from robertdfrench/tmux-2.2 
Tmux 2.2
 2016-06-20 09:36:55 -07:00
Todd Gamblin
8bdb6695c7 Merge pull request #1079 from davydden/pkg/blas_mpi_fortran 
require fortran compilers for Openblas and Openmpi
 2016-06-20 09:36:23 -07:00
Todd Gamblin
ce105e9bbe Merge branch 'bugfix/compiler_find' into develop 2016-06-20 09:34:25 -07:00
Todd Gamblin
84e21703bd Test no longer assumes compilers exist in /usr. 
- makes a fake gcc instead, and tests that.
 2016-06-20 09:28:39 -07:00
Robert.French
83b0c16728 Tmux 2.2 with PEP8 
Tmux 2.2

Provide variant to skip utempter

Remove utempter variant; 2.2 doesn't need it

Flake8ify
 2016-06-20 16:26:49 +00:00
Ben Boeckel
973caa3a07 modules.yaml: use the right envvar for pkg-config 
Fixes #1072.
 2016-06-20 11:10:29 -04:00
Denis Davydov
cf4a34c657 openmpi: raise an error without Fortran compiler 2016-06-19 11:59:29 +02:00
Denis Davydov
1cc04cff27 openblas: raise an error without Fortran compiler 2016-06-19 11:59:10 +02:00
Mario Melara
64c83638ff Adding test to list of test_names 2016-06-18 11:11:46 -07:00
Mario Melara
15e6b88a8b Adding new tests for compiler command for spack's test suite 2016-06-18 10:51:38 -07:00
Mario Melara
36275f8e6e More clean up of init_config, also no need for a different find_compilers function. 2016-06-18 10:50:55 -07:00
Mario Melara
ccb62b4620 Getting rid of no longer used init_config arg 2016-06-18 10:49:39 -07:00
Todd Gamblin
f9efb746d7 Merge pull request #1032 from eschnett/eschnett/cc-quotes 
Add quotes around file name
 2016-06-18 08:57:18 -07:00
Mario Melara
8af1c5fc8f Merge remote-tracking branch 'upstream/develop' into develop 
"Updating NERSC branch"
 2016-06-18 00:52:06 -07:00
Mario Melara
c703bfb54d Got rid of init_config flag since we don't need it. Instead we update the cache config if there are any changes 2016-06-18 00:48:08 -07:00
Todd Gamblin
62b2f2a7c9 Merge pull request #1065 from epfl-scitas/packages/espresso_update 
espresso : update to 5.4.0
 2016-06-17 14:51:45 -07:00
Todd Gamblin
4569df025e Merge pull request #1060 from mathstuf/no-break-long-words 
tty: do not break long words
 2016-06-17 14:51:26 -07:00
Todd Gamblin
9a8d109650 Merge pull request #1044 from adamjstewart/features/sncosmo 
Add py-sncosmo package
 2016-06-17 14:50:37 -07:00
Todd Gamblin
d7f48e1ff0 Merge pull request #1061 from mathstuf/reindex-preserve-explicit 
reindex: preserve 'explicit' flags
 2016-06-17 14:29:47 -07:00
Todd Gamblin
0bbbfc2ef7 Merge pull request #946 from LLNL/features/intel2 
Intel software packages and license enhancements
 2016-06-17 14:28:39 -07:00
Adam J. Stewart
536fa73d5f Python flake8 overhaul 2016-06-17 13:33:09 -05:00
Robert D. French
448f8c43d4 Added working Ferret spec 
Fixed ferret spec. It builds now

Made ferret spec more flake8-y

Fixed homepage and info text about Ferret

Removed vim swap file

Reverted changes to netcdf-fortran spec and added netcdf~mpi dependency to ferret spec to compensate for it

Fixed flake8 issues!
 2016-06-17 14:23:50 -04:00
Mario Melara
fe5eec5230 'find and 'add' are options for adding compilers via command line 2016-06-17 09:16:03 -07:00
Adam J. Stewart
80d444624b Fix activation of sites.py for sncosmo 2016-06-17 11:08:16 -05:00
Adam J. Stewart
24f65c502e Add additional Astropy dependencies 2016-06-17 10:45:10 -05:00
Adam J. Stewart
b2aa78d6ab Remove version constraints 2016-06-17 10:45:10 -05:00
Adam J. Stewart
4eeaff175c Allow packages to build 2016-06-17 10:44:28 -05:00
Adam J. Stewart
a660c60eb1 Add py-sncosmo package 2016-06-17 10:43:34 -05:00
Glenn Johnson
8970785d33 Add 'jdk' as a dependency. 
Add jdk as a dependency so that R has support for java and allow
packages that need java to work.
 2016-06-16 23:08:55 -05:00
Glenn Johnson
a813f03955 Add list_url for old versions. 2016-06-16 23:08:55 -05:00
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