Commit Graph

3817 Commits

Author SHA1 Message Date
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
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
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
Greg Lee
e4525e57bb intel parallel studio itac fixes 2016-07-25 14:02:15 -07:00
Greg Lee
dba384108b intel parallel studio setup mkl environment 2016-07-25 14:01:49 -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
Glenn Johnson
eb865b0df2 Add py-setuptools as dependency
With the addition of dependency types and with `py-setuptools` set as
type='build' there are more packages that need to have `py-setuptools`
added as a dependency.

This PR adds that dependency for the following packages:
- py-h5py
- py-networkx
- py-pytables
- py-scikit-image
2016-07-25 11:23:09 -05:00
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
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
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
Adam J. Stewart
1be486c90a Add CGNS package 2016-07-22 17:02:45 -05:00
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
Mitchell Devlin
796308ed85 edit 2016-07-21 13:39:27 -05:00
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
mwilliammyers
b8444aa518 Merge remote-tracking branch 'upstream/develop' into package-opencv
* upstream/develop: (126 commits)
  Fix indent/flake8 error.
  openexr : Add new package
  Set environment variables
  Added gnu packages datamash, parallel, and screen
  added package as argument to setup_platform_environment
  ilmbase : Add new IlmBase package
  Documented linker default
  fixed flake errors
  removed commented-out code
  Set default link type to dynamic on cray. Includes hooks for platform-based environment changes
  fixed flake errors
  fixed flake errors
  Improved cray_xc detection bug fix
  Improved cray_xc detection
  remove FIXMEs
  Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10
  Re-ignore licenses directory
  Add "default" configuration scope.
  Draft CDO
  Make frontend OS on Cray machines a proper linux distro.
  ...
2016-07-20 18:34:53 -06:00
mwilliammyers
a09bebcaea opencv : Add section comments 2016-07-20 18:19:59 -06:00