Commit graph

6909 commits

Author SHA1 Message Date
Todd Gamblin
b8b14c84e0 Bugfix: restore __contains__ method after ArchSpec refactor. (#2481) 2016-12-04 16:22:16 -08:00
George Hartzell
f0dcb5bbf7 Update go to 1.7.4 and 1.6.4 to fix security issues (#2467)
* Update go to 1.7.4 and 1.6.4 to fix security issues

The go team recently rolled out two releases to address security
issues.  Details available on the [go release
site](https://golang.org/doc/devel/release.html).

This commit updates our explicitly supported versions.

It also includes a comment about two CentOS requirements (enable
user_namespace and ensure that the static c library is installed) that
are required for the pacakges to pass their tests.

* Flake8 cleanup
2016-12-03 16:44:03 -08:00
Andrey Prokopenko
f17c22dfb5 zlib: added 'pic' variant (#2470)
It looks more complicated because zlib has custom configure which does
not support CFLAGS option. So instead, we take it from environment.
2016-12-03 16:43:44 -08:00
George Hartzell
6ddc518417 Update git package to include 2.11.0 (#2471) 2016-12-03 16:41:12 -08:00
Joseph Ciurej
552b4eae9e Fixes to Handling Multiple Architectures (#2261)
* Added some notes about how multiarch detection could be fixed.

* Implemented a preliminary version of the "spack.spec.ArchSpec" class.

* Updated the "spack.spec.Spec" class to use "ArchSpec" instead of "Arch".

* Fixed a number of small bugs in the "spack.spec.ArchSpec" class.

* Fixed the 'Concretizer.concretize_architecture' method so that it uses the new architecture specs.

* Updated the package class to properly use arch specs.
Removed a number of unused architecture functions.

* Fixed up a number of bugs that were causing the regression tests to fail.
Added a couple of additional regression tests related to architecture parsing/specification.
Fixed a few bugs with setting reserved os/target values on "ArchSpec" objects.
Removed a number of unnecessary functions in the "spack.architecture" and "spack.concretize" modules.

* Fixed a few bugs with reading architecture information from specs.
Updated the tests to use a uniform architecture to improve reliability.
Fixed a few minor style issues.

* Adapted the compiler component of Spack to use arch specs.

* Implemented more test cases for the extended architecture spec features.
Improved error detection for multiple arch components in a spec.

* Fix for backwards compatibility with v0.8 and prior

* Changed os to unknown for compatibility specs

* Use `spack09` instead of `spackcompat` for the platform of old specs.
2016-12-03 15:38:31 -08:00
hegner
2f46613132 Fix download URL and dependencies for py-pypar (#2430)
* fix download URL and dependencies for py-pypar

* use url_for_version in py-pypar
2016-12-02 13:56:00 -08:00
Nicolas Richart
cc92b9a3a2 foam-extend: modification to accept flex version >= 2.6 (#2452)
* Modification to accept flex version >= 2.6 + bug fix on paraview dependency

* flake8 "corrections"
2016-12-02 13:51:03 -08:00
Elizabeth Fischer
18878a8615 doxygen: Disable unnecessary graphviz dependency by default. (#2323) 2016-12-02 10:56:40 -08:00
Jon Rood
8b612d3568 Updating SuperLU package to use pic_flag instead of -fPIC, and removing specific version for default install method. (#2456) 2016-12-02 10:47:35 -08:00
Jon Rood
946605a4c9 Updating yaml-cpp from Package to CMakePackage. (#2457) 2016-12-02 10:41:18 -08:00
Gregory Lee
84dc0b5b83 new intel parallel studio versions (#2459) 2016-12-02 10:35:36 -08:00
Andrey Prokopenko
3024c0096a cmake: update the requirements for --no-system-jsoncpp option (#2312)
The option appeared in CMake 3.2 (specifically, in 3.2.0-rc2, see
https://cmake.org/pipermail/cmake-developers/2015-February/024552.html).
2016-12-01 17:51:00 -08:00
George Hartzell
c01f78e515 Make X11 font install dir the font search default (#2203)
* Make X11 font install dir the font search default

We install the X11 fonts into `/share/fonts` beneath the font-util
installation prefix, but that directory is not one of the places that
the font subsystem searches.

This commit makes the fontconfig package depend on the font-util
package, and then it makes

```python
spec['font-util'].prefix + "/share/fonts"
```

be the fontconfig default font location.

Before this change, plots drawn by R have bounding boxes where font
glyphs should be.  After this change fonts appear as expected.

* Enrich description string (trigger new CI run)

Improve the docstring for the package.

Also interested in the side effect of triggering another CI run
to see if the recent flake8 fix lets this PR run clean.

* Flake8 cleanups
2016-12-01 17:38:00 -08:00
hegner
8dae60c5f0 Fix py-scientificpython and py-argcomplete dependencies (#2420)
* add missing py-numpy dependency to scipy

* add missing setuptools build dependency to py-argcomplete
2016-12-01 14:34:07 -08:00
Sergey Kosukhin
c6e2d9c1b0 Updated hdf5: new versions added. (#2442)
* Updated hdf5: new versions added.

* Updated hdf5: url_for_version() accounts for per-version urls.
2016-12-01 14:31:27 -08:00
Matt Belhorn
e26a0be731 Does nothing if no prexisting config.guess is found. (#2446)
* Does nothing if no prexisting config.guess is found.

* Update name for RHEL OS.
2016-12-01 11:54:48 -06:00
TomasPuverle
f1fe614d67 Update tutorial_sc16_packaging.rst (#2450)
Fixed a typo.
2016-12-01 11:53:18 -06:00
TomasPuverle
a961797155 Update workflows.rst (#2451)
Fixed a typo.
2016-12-01 11:53:03 -06:00
Sergey Kosukhin
051720defd More informative help messages for spack config. (#2453) 2016-12-01 11:52:56 -06:00
Bruno Turcksin
bc4237c93e Update trilinos version to 12.10.1 (#2454) 2016-12-01 11:52:05 -06:00
Denis Davydov
6ce0ee49a9 likwid: add new package (#2455) 2016-12-01 11:51:23 -06:00
Gregory Lee
8e816f8f88 Merge pull request #2364 from davydden/ips_mkl
intel-parallel-studio: fix location of MKL libs
2016-12-01 09:21:37 -08:00
George Hartzell
8ab69c4d32 Update R&friends to use our X11 libs (#2053)
* Update R&friends to use our X11 libs

Add `depends_on()`'s for R, Cairo, and Tk so that they use the Spack X
bits.

* Conditionalize X stuff on variant

Another step towards hooking up the X stuff.

There's still discussion happening on the issue, but this is better
than the 'everything must build with X' state that it was in.
2016-11-30 15:49:49 -06:00
Adam J. Stewart
6cc9b31747 Allow shell support to work when set -u is set (#2418) 2016-11-29 17:04:29 -08:00
Javier
5eb7026dd1 New package - r-irkernel (#2434)
* New package - r-irkernel

* New package - r-pbdzmq, dependency of r-irkernel

* Adding blank line expected by flake8 tests
2016-11-29 16:59:28 -08:00
Joseph Ciurej
3d439d8946 Added the '+debug' and '+except' variants to the 'tetgen' package. (#2370)
Fixed a bug that was causing memory errors after asserts in 'tetgen@1.5.0'.
2016-11-29 16:18:03 -06:00
hegner
c3e34b480a CDash fixes (#2438)
use short spec instead of spec as CDash has a limitation in name length
mark all problems as 'FAILED' as CDash does not understand "ERRORED" status
2016-11-29 13:30:59 -06:00
Javier
e3778923b6 New package - r-rbokeh (#2436) 2016-11-29 11:29:46 -06:00
Erik Schnetter
00ad8e87f4 jemalloc: Update to 4.3.1 (#2435)
This corrects a severe problem (segfault) on macos Sierra.
2016-11-29 09:51:55 -06:00
Barry Smith
4d56d4f1f9 add support for installing the development (master) version of PETSc (#2431)
Funded-by:  IDEAS
Project:  IDEAS/xSDK
Time:   .3 hours
x
2016-11-29 09:28:09 -06:00
hegner
a6d579ea15 add headers neede for CDASH to junit output (#2433) 2016-11-29 08:29:57 -06:00
Adam J. Stewart
664939eeba Fix building latest version of flex (#2401)
* Fix building latest version of flex

* Don't need when clause

* Remove perl deps, shebang too long
2016-11-28 09:48:34 -08:00
hegner
a2e6de9b5d add missing zeromq dependency to r-rzmq (#2425) 2016-11-28 09:14:16 -08:00
Javier
bb5bd8091d New package - r-pryr (#2424) 2016-11-28 09:14:10 -08:00
Javier
2d43b56deb New package - r-uuid (#2423) 2016-11-28 09:14:05 -08:00
Javier
6e68a01e50 New package - r-rmarkdown (#2422) 2016-11-28 09:14:00 -08:00
Javier
6c2729ae6f New package - r-repr (#2421) 2016-11-28 09:13:20 -08:00
Denis Davydov
d2d23b76da hdf5: fix for lib64 installation (#2349) 2016-11-28 09:12:48 -08:00
Denis Davydov
b47bd9cc00 scotch: fix compilation on macOS (#2326) 2016-11-26 16:48:50 -08:00
Javier
eeb9c84677 New package - r-rinside (#2416)
* New package - r-rinside

* Changes to pass flake8 test
2016-11-26 16:48:04 -08:00
Javier
1cdfc30374 New package - r-rsnns (#2415) 2016-11-26 16:47:56 -08:00
Javier
0c4e97b6a1 New package - r-rzmq (#2414)
* New package - r-rzmq

* Adding homepage
2016-11-26 16:47:47 -08:00
Javier
7baa6e824b New package - r-irdisplay (#2413) 2016-11-26 16:47:38 -08:00
Javier
cc0d08255c New package - r-hexbin (#2412) 2016-11-26 16:47:25 -08:00
Andrey Prokopenko
8f0b91edaa netcdf: multiple improvements (#2377)
- Added 'dap' and 'cdmremote' variants
  This is based on work in #2324 with the following motivation:
      Turn off DAP support by deafult.  DAP requires curl, which has issues
      with circular dependencies.  For 95% of NetCDF users that do not need
      DAP, turning it off avoides this rats nest of problems.
- Added 'parallel-netcdf' variant
  To support work with parallel-netcdf
- Added 'shared' and 'static' build separation
2016-11-24 13:52:28 -08:00
George Hartzell
cde8f697a9 Bugfix/update go packages (#2369)
* Update go-bootstrap package

The last C based Go src tree was the 1.4 series.  For a while they
were cutting new releases so that people could bootstrap from a C only
system.  Now they're recommending that you either use the release-1.4
branch or that you use a date-stamped tarball that they'll produce on
an as-needed basis.

There are several issues that keep 1.4.2 from building on a CentOS 7
system.

I've switched to the date based tarball.

The cgo bits were also mis-behaving, but they're not needed for the
bootstrapping task so I've set an environment variable that disables
them.

Details [on the install-from-source
page](https://golang.org/doc/install/source#go14) and these issues:

- https://github.com/golang/go/issues/17545
- https://github.com/golang/go/issues/16352.

* Update go package

Switched from pulling from the git repository to using the source
tarballs and added digest values.

Added support for 1.7.3, continued supporting 1.6.2, including patches
for a couple of problems (details in
[17545](https://github.com/golang/go/issues/17545) and
[17986](https://github.com/golang/go/issues/17986).

Dropped support for 1.5.4 and 1.4.2 because they no longer pass their
tests and the patches above to not apply.
2016-11-24 12:25:51 -08:00
Andrey Prokopenko
11bfccd53f Adding pic_flag property to compilers (#2375)
Different compilers have different flags for PIC (position-independent
code). This patch provides a common ground to accessing it inside specs.

See discussions in #508 and #2373. This patch does not address the issue
of mixed compilers as mentioned in #508.
2016-11-24 12:25:22 -08:00
scheibelp
261d36e801 Add dynamic search option for package sources (#2270)
Package provides a 'list_url' attribute which may be searched to find
download links. #1822 created a slowdown for all tests by always
searching this URL. This reenables dynamic search only in cases where
all other fetchers fail. This also only enables dynamic search when
'mirror_only' is set to false.
2016-11-24 12:21:05 -08:00
Javier
9c267e9c73 Updated version - r-lattice (#2410) 2016-11-24 12:19:42 -08:00
Javier
09a5826903 New package - r-testit (#2409) 2016-11-24 12:19:10 -08:00