Commit graph

4720 commits

Author SHA1 Message Date
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
500218df80 Merge pull request #1384 from epfl-scitas/qa/drop_flake8_python26
qa : no flake8 on python 2.6, coveralls only on python 2.7
2016-07-30 20:25:14 -07:00
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
Todd Gamblin
49e9f365d8 Merge pull request #1387 from glennpj/r-randomforest
New package r-randomforest
2016-07-30 20:12:21 -07:00
Todd Gamblin
0fa8a491d3 Merge pull request #1386 from glennpj/r-car
New package r-car
2016-07-30 20:12:02 -07:00
Glenn Johnson
41cd861861 New package - r-quantmod
Qualitative Financial modelling framework.
2016-07-30 18:25:43 -05:00
Glenn Johnson
2913aa8d09 New package - r-ggmap and dependencies
Spatial visualization with ggplot2
2016-07-30 18:14:02 -05:00
Glenn Johnson
1bd2def41e New package - r-maps
Draw geographical maps.
2016-07-30 17:34:07 -05:00
Glenn Johnson
386f0e577a New package - r-maptools
Tools for reading and handling spatial objects.
2016-07-30 17:26:31 -05:00
Glenn Johnson
7207ce2a18 New package - r-caret
Classification and Regression Training
2016-07-30 16:53:54 -05:00
Glenn Johnson
20e52e5052 New package - r-glmnet
Lasso and Elastic-Net Regularized Generalized Linear Models
2016-07-30 16:38:00 -05:00
Glenn Johnson
e9944150a5 New package - r-vcd
Visualizing Categorical Data
2016-07-30 16:28:43 -05:00
Glenn Johnson
fc1804974c New package - r-multcomp
Simultaneous Inference in General Parametric Models.
2016-07-30 16:09:57 -05:00
Glenn Johnson
12167e8f37 New package r-randomforest
Breiman and Cutler's Random Forests for Classification and Regression.
2016-07-30 15:39:28 -05:00
Glenn Johnson
8dc26bbcd9 Have R extensions build in parallel.
Set `MAKEFLAGS` so R extensions can be built in parallel if that is set
in spack.
2016-07-30 15:20:14 -05:00
Glenn Johnson
ee7acc6b13 New package r-car
Companion to Applied Regression.
2016-07-30 15:10:25 -05:00
alalazo
f4422dc165 qa : fixes #1370 (no flake8 on python 2.6, coveralls only python 2.7) 2016-07-30 18:49:23 +02:00
Matt Belhorn
dc7e0899a0 Invokes subshell without user init scripts. 2016-07-30 11:38:34 -04:00
Matt Belhorn
5bb2d3baa0 Replaces technique for obtaining default back_end target.
New technique parses output of `module list` in clean login environment
in order to let convoluted initialization scripts to work for us rather
than against us as when trying to parse them directly.
2016-07-29 15:06:56 -04:00
Matt Belhorn
5e97eb5ec4 Obtains default modules from a clean subshell.
The list of default environment modules is obtained by calling

`module list -lt`

from a subshell with a wiped environment. This allows `/etc/profile` and other
init scripts to be fully sourced which should generally include loading the
default modules.

The list of default modules is then parsed for the first acceptable CPU target,
assumed to be the back_end target.
2016-07-29 15:02:25 -04:00
Kelly (KT) Thompson
6c80b15220 GTK+3: Provide updates to package dependencies.
WIP: I started trying to build gtkplus@3.20, but this package has many more
dependencies than v2 and it requires newer versions of existing packages. This
commit provides updates for 5 packages that are required by GTK+3. This is not
the complete set of changes required for GTK+3.

atk  - move default version from 2.14 -> 2.20.
glib - move default version from 2.42 -> 2.49
     - v2.49 requires pcre+utf as a new dependency.
pcre - if variant +utf is selected, add '--enable-unicode-properties' to the
       configure options.
libepoxy - new package to spack
         - manages OpenGL function pointers.
pango    - move default version from 1.36 -> 1.40
2016-07-29 09:05:44 -06:00
Denis Davydov
aad5a4c4b3 mkl: flake8 fixes; minor docu update 2016-07-29 14:12:07 +02:00
Paul Hopkins
5eebb2defa Use space characters to separate preferred variants from package name and each other 2016-07-29 13:02:47 +01:00
Denis Davydov
b6ce0e6f0e trilinos: make sure hdf5 is picked up from Spack 2016-07-29 13:11:12 +02:00
Denis Davydov
943896e237 trilinos: fix lapack lib dir 2016-07-29 13:09:34 +02:00
Denis Davydov
8ee4df8101 hypre: minor cleanup related to blas/lapack 2016-07-29 11:37:19 +02:00
Denis Davydov
572f1cd427 mkl: symlink libs to prefix.lib 2016-07-29 11:36:37 +02:00
Todd Gamblin
e04662f84f Merge pull request #1344 from LLNL/bugfix/py-nose-nosetests
do not ignore nosetests script in py-nose
2016-07-28 10:19:13 -07:00
becker33
5caaa2cd75 Merge pull request #1331 from adamjstewart/fixes/mvapich2
MVAPICH2 depends on libpciaccess
2016-07-28 09:52:51 -07:00
becker33
3759f62cba Merge pull request #1235 from davydden/pkg/p4est_run_tests
p4est: use run_tests instead of a variant
2016-07-27 18:36:36 -07:00
Matt Belhorn
07f2dd5498 Merge pull request #1 from robertdfrench/olcf/unified_cray_platform
PEP8 Goodness
2016-07-27 14:33:09 -04:00
robertdfrench
eab56b71be PEP8 Goodness 2016-07-27 13:11:24 -04:00
Matt Belhorn
3040381f03 Front-end unification for Cray systems.
A platform to generically cover all Cray systems is introduced to avoid having
specific platforms for each of XK (XE, XT), XC, and future systems using CrayPE
and CNL.

The platform searches for 'front_end' and 'back_end' targets, in order, from:

  * Environment variables 'SPACK_FRONT_END' and 'SPACK_BACK_END'
  * A spack configuration file 'targets.yaml'
  * Parsing `/etc/bash.bashrc.local` for first loaded CrayPE CPU target.

If a back_end target is not found through one of these methods, an exception is
raised. Otherwise, the back_end is set as the default target. The shell init
script search is based on recommendations in Crayports case #144359.

No automagic way of determining front_end targets has been found (to date) so if
a front_end is not specified through configuration, it is ignored which should
leave a spack instance in a consistant state.
2016-07-27 11:37:15 -04:00
George Hartzell
f855cf6bab Add package for tree
Add a package for [tree](http://mama.indstate.edu/users/ice/tree/).

It has a Makefile that hardcodes a prefix and some CFLAGS.  Used
filter_file to:

- set the make variable *prefix* to `prefix`; and
- comment out their CFLAGS, just use ours....

It installs, runs on CentOS7, and uninstalls cleanly.
2016-07-27 11:32:03 -04:00
Matt Belhorn
b1e6c58ff2 Adds __str__ method to CNL operating system class. 2016-07-27 11:25:23 -04:00
Matt Belhorn
4e6fdd12e2 Adds targets config file 2016-07-27 11:25:23 -04:00
Todd Gamblin
458deaae5e Merge pull request #1350 from adamjstewart/fixes/openssl
Fix OpenSSL url_for_version
2016-07-27 08:08:00 -07:00
alalazo
9c7b98dcc8 modules : handle dashes in environment variables 2016-07-26 09:03:17 +02:00
Greg Lee
e4525e57bb intel parallel studio itac fixes 2016-07-25 14:02:15 -07:00