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Author SHA1 Message Date
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
Denis Davydov
aad5a4c4b3 mkl: flake8 fixes; minor docu update 2016-07-29 14:12:07 +02:00
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
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
Todd Gamblin
458deaae5e Merge pull request #1350 from adamjstewart/fixes/openssl 
Fix OpenSSL url_for_version
 2016-07-27 08:08:00 -07:00
becker33
e4ced765f1 Merge pull request #1353 from epfl-scitas/qa/minor_cleanup 
qa : minor cleanup
 2016-07-25 10:34:43 -07:00
Samuel Knight
a2d4dcc636 Added libhio package 2016-07-25 17:32:03 +00:00
becker33
969e785d94 Merge pull request #1352 from glennpj/r_googlevis 
New package - r-googlevis
 2016-07-25 10:25:47 -07:00
becker33
5b7ec8de95 Merge pull request #1351 from glennpj/r_htmlwidgets 
New packages - R htmlwidgets
 2016-07-25 10:25:19 -07:00
becker33
e19872e77f Merge pull request #1347 from glennpj/rdeps 
Add dependency type to r- packages
 2016-07-25 10:19:32 -07:00
George Hartzell
d684b17c06 Fix doc for install_tree (cut/paste error) 
It looks like the docs for copy_tree were cut/paste from copy and still referred to installing a "file".

This fixes that.
 2016-07-25 08:45:44 -07:00
alalazo
5cfaa557d3 qa : flake8 issues 2016-07-25 10:19:58 +02:00
alalazo
23006d1195 spec : removed dead code 2016-07-25 09:05:50 +02:00
Glenn Johnson
81cd458c26 r-curl update and chaged remote archive 
This updates to the 1.0 version of r-curl. The remote archive directory
name also changed so change that here as well.
 2016-07-24 16:48:07 -05:00
Glenn Johnson
27986c9edf New packages - R htmlwidgets 2016-07-24 16:43:35 -05:00
Glenn Johnson
b7bf88c761 New package - r-googlevis 2016-07-24 16:38:36 -05:00
Adam J. Stewart
29278090eb Fix OpenSSL url_for_version 2016-07-24 15:19:27 -05:00
Glenn Johnson
b1e5ec0573 Make sure package has the url attribute. 
In addition to `list_url` make sure the package has the `url` attribute
set before attempting to add urls from a list. This is to cover the case
where there may be a `list_url` specified in tandem with a
`url_for_version`.
 2016-07-24 09:21:11 -05:00
Glenn Johnson
4f09e8c975 Only use list if list_url set 
This commit will make urls from list_url only checked if `list_url` is
set in the package file. This makes more sense as there is no need to
check for those if the attribute is not present. If `url` is present and
`list_url` is not then it would result in the same url. If
`url_for_version` is used then that will not work anyway.
 2016-07-23 22:56:08 -05:00
Glenn Johnson
a8855f48aa Add dependency type tp r- packages 
This PR adds the `nolink` dependency type to r- package dependencies.
This is needed due to the new dependency types in Spack. A couple of
packages were updated with new versions as well.
 2016-07-23 19:43:55 -05:00
Glenn Johnson
4181fd79cd Fix flake8 errors related to lines 
Fixed the flake 8 errors that involved too many blank lines or not
enough blank lines. Basically, all of the flake8 errors except line
length errors.
 2016-07-23 19:10:09 -05:00
Glenn Johnson
b51be2bb1b Have fetch use list_url 
This PR allows archive file retrieval from urls derived from the
`list_url` setting in a package file. This allows for continued
retrieval of checksummed archive files even when they are moved to a new
remote location when a package is updated upstream.
 2016-07-23 19:09:58 -05:00
Greg Lee
773bca159a do not ignore nosetests script in py-nose 2016-07-22 15:49:36 -07:00
Glenn Johnson
ec9959b152 R extension dependencies with compiler wrapper 
This commit introduces a mechanism to insure that R package dependencies
are built with the Spack compiler wrapper. A copy of Makeconf is made
before `filter_compilers` is called. This is then pointed to by the
R_MAKEVARS_SITE environment variable set up in
`setup_dependent_environment`. With this the normal compilers are used
outside of spack and the spack wrapper compilers are used inside of
spack.

This commit also standardizes on the `join_path` call. It also sets the
commented build command to reflect what is actually used with the newer
string formatting.
 2016-07-22 17:05:01 -05:00
becker33
7220bc1766 Merge pull request #1340 from adamjstewart/features/create 
Use example deptypes in newly created packages
 2016-07-22 14:25:12 -07:00
Todd Gamblin
395c616a48 Merge pull request #950 from xjrc/packages/python 
Enhancement Proposal: Make Python Spack Installs Ignore User Configuration
 2016-07-22 13:56:19 -07:00
Adam J. Stewart
ebbcebac62 Use example deptypes in newly created packages 2016-07-22 13:55:00 -05:00
Joseph Ciurej
fa92f58167 Adding temporary script that fixes all Python extensions w/ 'setup_py'. 2016-07-22 11:17:19 -07:00
Joseph Ciurej
ac2e0962ce Improved the build flag construction code in the python install method. 2016-07-22 11:12:02 -07:00