Commit graph

2013 commits

Author SHA1 Message Date
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
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
ee7acc6b13 New package r-car
Companion to Applied Regression.
2016-07-30 15:10:25 -05:00
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
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
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
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
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
Greg Lee
773bca159a do not ignore nosetests script in py-nose 2016-07-22 15:49:36 -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
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
Joseph Ciurej
fb2d2303d6 Fixed a bug that was causing Python installs to be affected by user config. 2016-07-22 11:11:08 -07:00
Todd Gamblin
f5b4664c7c Merge pull request #1336 from glennpj/rcase
Fix alpha case of dependencies for some r-packages
2016-07-22 10:08:14 -07:00
Todd Gamblin
adffba5081 Merge pull request #1230 from hartzell/update-jdk
Add URL and md5 for jdk-8u92.
2016-07-21 22:06:29 -07:00
Glenn Johnson
e083c91d5e Fix alpha case of dependencies.
A while ago I was asked to convert packages to all lowercase. That was
done but some dependencies did not get converted in the specification.
This commit fixes that as well as a couple of urls that need to be made
explicit and a missing dependency on jdk.
2016-07-21 19:58:04 -05:00
Todd Gamblin
ed737cb2a2 Merge pull request #1333 from LLNL/features/no-openssl-pinging
Remove remote website pinging from OpenSSL
2016-07-21 16:46:59 -07:00
Todd Gamblin
488550c2e6 Merge pull request #1334 from hartzell/add-gcc-5.4.0
Update gcc package with info about gcc-5.4.0
2016-07-21 16:37:31 -07:00
Todd Gamblin
8523f75e6c Remove remote website pinging from OpenSSL
- OpenSSL no longer checks remote versions on the openssl site.

- Spack is used on systems that aren't connected to the internet, and
  this check is probably in the wrong place and affects too many
  commands.  We can work on figuring out a better, more configurable
  place to put a check like this.
2016-07-21 16:35:20 -07:00
George Hartzell
4efe022165 Update with info about gcc-5.4.0 2016-07-21 15:36:22 -04:00
George Hartzell
4c105895ab Fix flake8 violations 2016-07-21 14:24:51 -04:00
George Hartzell
9523e50732 Fix shebang line in tcl scripts
Lmod's configure script goes to the trouble of finding
tclsh.  This change uses that info to rewrite the #! lines
in the tcl scripts so that they call the tclsh that the
configure script discovered.

It needs to massage the existing shebang lines into something
that the sed statement in the makefile can manipulate and
it needs to add the path_to_tclsh info into the set of sed
statements.

Checked with versions 6.4.1 and 6.3.7 (the checksum for 6.0.1 is
incorrect, a fix for another time).
2016-07-21 13:58:16 -04:00
George Hartzell
52f0249c61 tcl is actually a runtime dependency.
lmod uses tclsh at runtime, so adjust the depends_on accordingly
(thanks @davydden!).
2016-07-21 13:51:03 -04:00
George Hartzell
a27cb639d8 The lmod package should depend_on('tcl')
The lmod package needs a tclsh.  Up until now it just assumed
that one was available on the system.

This change adds a depends_on('tcl') to the lmod package.

The tcl package installs a tclsh script with an embedded version
number (e.g. tclsh8.6) but the lmod configuration looks for tclsh.
This change extends the tcl package to symlink tclshX.Y to tclsh in
the tcl package bin directory.
2016-07-21 13:51:03 -04:00
Adam J. Stewart
cf8f14780f MVAPICH2 depends on libpciaccess 2016-07-21 11:13:17 -05:00
Glenn Johnson
ead1b93f75 MPI related changes
- Redid the code for setting the itac symlink for the cluster edition.
- Removed the *PATH variables for MPI to avoid a conflict with other MPI
  environment modules.
- Added missing test for `+all` when checking variants.
2016-07-20 20:03:05 -05:00
Glenn Johnson
0be4c7dfbd Changes as discussed in PR review
- removed unneeded entry for `debugger/gdb/intel64_mic`
- set `+mpi` directory name to impi
2016-07-20 20:03:05 -05:00
Glenn Johnson
5e5e36a659 Fix flake8 errors. 2016-07-20 19:54:35 -05:00
Glenn Johnson
16f67b5bb1 Setup environment for Intel Parallel Studio
Set up the environment for the Intel compilers and tools. This commit
does the following:

- Unset variables that were incorrect from the auto guess prefix
  inspections.
- Add a RemovePath environment_modifications_formats for dotkit.
- Set the module environment variables appropriate for the different
  variants.
- Change the component logic so that the '+all' variant works. It was
  getting split by letter and leaving COMPONENTS empty.
- Added a variant checking function.
- Added NONRPM_DB_DIR to the silent.cfg so that the product database
  goes to the installation directory.
- With the product database in prefix the code to remove the product
  database file from the home directory is no longer needed and was
  removed.
- Reformat the 'tools' variant description.

There are probably more variables needed for the '+tools' for the
'professional' product version but I do not have access to that.
2016-07-20 19:54:35 -05:00
Todd Gamblin
e389afedaa Merge pull request #1323 from glennpj/rlib
Set environment variables for R
2016-07-20 15:43:26 -07:00
Todd Gamblin
b9c79824a2 Merge pull request #1313 from sknigh/gnu-tools
Added packages for GNU tools screen, datamash, and parallel
2016-07-20 15:38:55 -07:00
Todd Gamblin
0777d3a5ba Merge pull request #1326 from mwilliammyers/package-openexr
openexr : Add new package
2016-07-20 15:35:36 -07:00
Glenn Johnson
0c75174ec3 Fix indent/flake8 error. 2016-07-20 15:56:20 -05:00
mwilliammyers
e973adf84b openexr : Add new package 2016-07-20 14:49:03 -06:00
Glenn Johnson
f9137f606f Set environment variables
This commit adds `setup_environment` to export the libraries and
headers.

Fixes #1314.
2016-07-20 15:37:31 -05:00
Todd Gamblin
d8acd41ba1 Merge pull request #1321 from mwilliammyers/package-ilmbase
ilmbase : Add new IlmBase package
2016-07-20 13:13:21 -07:00
Todd Gamblin
8efbec3c0b Merge pull request #1292 from eschnett/eschnett/hdf5-default-1.10
Make newest HDF5 release the default version
2016-07-20 12:57:45 -07:00