Commit graph

10421 commits

Author SHA1 Message Date
Oliver Breitwieser
3cf998a5db Add tmux@2.8 (#10010) 2018-12-04 08:37:09 -06:00
Greg Sjaardema
231888f3e9 PNETCDF: Update with current versions (#9982)
* PNETCDF: Update with current versions

Added latest versions. (1.10.0, 1.9.0, 1.8.1)

* PNETCDF: Revert version change in url

Reverted the change in the url variable version since not required.
2018-12-04 08:31:41 -06:00
Greg Sjaardema
6e3b016aa2 NETCDF: Add new versions and update url (#9970)
* NETCDF: Add new versions and update url

Added the 4.6.2 version which was recently released.
Changed the url to point to the official Unidata site and added option to retrieve master version from git.

* NETCDF: checksum and version updates

Reverted back to use of previous URL.  The `https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz` location is newer, but spack does not seem to be able to access all of the versions at that location -- only goes back to 4.5.0.  Since several installations are still providing 4.4.0, thought it best to go back to previous url.  However, it looks like the naming convention has changed since 4.6.2, so need to provide explicit url for 4.6.2.  Probably best to go to a `url_for_version()` scheme if that naming convention stays in place?
2018-12-04 15:03:25 +01:00
Bert Wesarg
262b3f859e boost: 1.68 also needs boost_1.67.0_pgi.patch (#9980)
Its in upstream with the upcoming 1.69 release though.
2018-12-04 14:49:20 +01:00
Peter Scheibel
34f64f1f3f improved constraint conflict error message (#9975) 2018-12-04 14:19:57 +01:00
Matthias Wolf
e3aa36f4cb fix: adapt junit template to escape std{out,err} (#9935) 2018-12-04 14:05:45 +01:00
George Hartzell
0c3f220fb1 Disallow bcl2fastq2 on OS X (#9966)
* Disallow bcl2fastq2 on OS X

[Illumina's computing requirements][reqs] claim support for RHEL/CentOS and
go on to say:

> May be possible to install and run on other 64-bit Linux distributions or Unix variants.

The sufficient issue is its reliance of malloc.h.  There may be more.

[reqs]: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/computing-requirements.html

* Add an informative msg for the user
2018-12-04 13:44:15 +01:00
Neil Flood
e3d204cb8f Expand dependency on qt to allow qt4 (#9964) 2018-12-04 13:37:37 +01:00
Satish Balay
808c2ea5ce petsc: when petsc is built with fortran [default in spack] its best to use hdf5+fortran (#9986) 2018-12-04 13:32:30 +01:00
Neil Flood
47b7016ea7 r-optparse: new package (#9967) 2018-12-04 13:20:08 +01:00
Nick Forrington
9551b34cb5 pgi: Add checksum for PGI 18.10 (#9985) 2018-12-04 13:12:20 +01:00
Matthias Diener
dfb02fd078 cmake: add version 3.13.1 (#9983) 2018-12-04 13:09:49 +01:00
Levi Baber
27e8fcb945 abyss: new version (#9981) 2018-12-04 13:02:36 +01:00
sknigh
a9695bac50 Added missing libtool dependencies to libvterm and unibilium (#10007) 2018-12-04 13:01:37 +01:00
Robert Maynard
0d033a042c Download CMake sources from the Github releases (#10003)
Now that CMake is providing CMake release artifacts on github,
we should prefer those as they have better download speeds and
uptime.
2018-12-03 12:35:51 -06:00
jthies
3a2045b7c0 Phist 1.7.4 (#9996)
* packages/phist: new version 1.7.4 with new variant 'host' to enable/disable host-specific optimizations.
2018-12-03 09:40:51 -06:00
HAOCHENG LIU
66a62d82c4 Bump vtkm to version 1.3 and add new features (#9968)
This commit allows users to enable openmp, rendering, logging and mpi
in vtkm. Meanwhile, it adds support for cuda architecture selection.

[VTK-m 1.3 Release notes](https://gitlab.kitware.com/vtk/vtk-m/tags/v1.3.0)
2018-11-30 19:48:22 -08:00
Mark W. Krentel
cc5446f25c hpctoolkit: overhaul to use spack dependencies (#9946)
Overhaul hpctoolkit to AutotoolsPackage and to build its dependencies
directly from spack instead of using hpctoolkit-externals.

Remove hpctoolkit-externals since it's no longer needed.
2018-11-30 18:11:12 -08:00
jwallior
930debcf35 New versions for a few python modules (#9969)
* py-jupyter-console: Add version 5.2.0

* py-jupyter-core: add version 4.4.0

* py-lxml: add version 4.2.5

* py-zmq: add version 17.1.2

* py-terminado: add version 0.8.1

* py-pexpect: add version 4.6.0

* py-pytables: add version 3.4.4
2018-11-28 21:44:15 -06:00
Piotr Luszczek
8375b5b571 Add PLASMA version 18.11.0 and Lua variant (#9689)
* Add PLASMA 18.11.1 with optional Lua and test for headers
2018-11-28 16:59:05 -06:00
Ondřej Čertík
62f1cf3678 Add f18 package (#9183)
* Add f18 package

* Fix flake8 errors

* Install the f18 binary into prefix.bin by hand

* Add spack-build into the path

* Fix the license header
2018-11-28 14:13:30 -06:00
Massimiliano Culpo
e998a399da Injected flags have a consistent order (#9960)
Fixes #9908

Spack was assembling flags in a manner that could in different
orderings for repeated concretizations of the same spec and config
2018-11-28 10:23:38 -08:00
Michael Kuhn
5cea4a75d7 glib: disable SELinux explicitly (#9956) 2018-11-28 10:06:17 +01:00
George Hartzell
e4e980ee97 bcl2fastq2 package: recursively delete after copy (#9959)
Fixes #9944

73c978d replaced a move with a copy, which cased rmdir to fail (as
it expects an empty directory). This switches to use `shutil.rmtree`
instead.
2018-11-27 17:22:14 -08:00
Scott Wittenburg
33b112a60d Expose option to save all dependencies when writing spec.yaml (#9965) 2018-11-27 17:13:39 -08:00
Jon Rood
4c3091b05e Fixing problems with lammps dependencies voropp and latte (#9909)
* Fixing problems with lammps dependencies voropp and latte.

* Always replacing CFLAGS in voropp and specifying voropp+pic dependency in lammps.
2018-11-27 16:55:21 -07:00
Matthias Diener
2164181d0a git: add version 2.19.2 (#9961)
Also fixes instructions for new releases
2018-11-27 16:32:22 -06:00
Neil Flood
8a78c9c6bc Rename py-proj to py-pyproj, consistent with Spack's current naming conventions (#9962) 2018-11-27 16:31:30 -06:00
thelfer
2e04f3daab new package: add support for the tfel package (#9930) 2018-11-27 07:16:55 +01:00
Michael Kuhn
16d3e44515 py-pygobject: add missing pkgconfig dependency (#9955) 2018-11-26 21:41:44 -06:00
Axel Huebl
b26c85301d OpenMPI: Prefer Last 3.X (#9945)
The latest OpenMPI release, v4.0.0, does not build with many GCC
variants. Since this is our default, a lot of users get hit.

Let's wait for some point releases.
2018-11-26 16:46:04 -06:00
Eric
20a6dde10b GATK: Add version 4.0.11.0 (#9953) 2018-11-26 14:54:05 -06:00
Eric
d9046e70c1 minced: Add version 0.1.6 (#9951) 2018-11-26 14:22:17 -06:00
Matthias Diener
bab3d7734a hdf5: add version 1.8.21 (#9952) 2018-11-26 12:56:44 -06:00
Michael Kuhn
7df14134c1 go: add 1.11.2 (#9948) 2018-11-26 11:33:55 -06:00
Eric
5cd8233139 metabat: Add version 2.11.2 (#9950) 2018-11-26 11:32:14 -06:00
Miles Perry
28e93a7a79 Feature/gatk (#9872)
* added 3.8-1 version

* fixed flake8 stuff
2018-11-26 11:30:21 -06:00
Adam J. Stewart
06dcf72f14 Uncomment dependencies previously disallowed by concretizer (#9942) 2018-11-26 09:11:16 +01:00
Sinan
096922c39d Package/py scikit learn (#9843)
* add v0.20 specific dependency versions, also add cython and py-test as dependencies

* make flake8 happy

* make cython a build-only dependency
2018-11-24 19:03:30 -06:00
Neil Flood
4c1733bff4 py-pygresql: new package (#9922)
* py-pygresql: new package

* Added dependency on py-setuptools, as the build will use it if present
2018-11-24 17:45:27 -06:00
Neil Flood
e3e01ab3d7 py-psycopg2: new package (#9926)
* py-psycopg2: new package

* Added dependency on py-setuptools, as the build will use it if present
2018-11-24 17:45:16 -06:00
Denis Davydov
058a772a52 p4est: fix a typo (#9932) 2018-11-24 17:45:04 -06:00
Matthias Diener
9d2ea84112 mc: add version 4.8.21 (#9943) 2018-11-24 17:42:46 -06:00
Matthias Diener
e86a28aff7 intel-parallel-studio: add missing updates to 2019.1 (#9941) 2018-11-24 15:44:57 -06:00
Neil Flood
9945a59c47 py-geopandas: New package. (#9919)
* py-geopandas: New package, including packages for its dependencies

* Trailing whitespace removed, etc

* One more trailing whitespace

* Removed some extraneous dependencies. No idea why I thought I needed them, but it now builds fine without them.

* Added a variant +plotting, to include the dependencies required for plotting, as these are large-ish if not being used.

* Added explicit dependency on py-matplotlib
2018-11-24 15:44:44 -06:00
Matthias Diener
25b9938ad1 cmake: add version 3.13.0 (#9940) 2018-11-24 14:23:10 -06:00
Neil Flood
a0fc573ff4 r-geor: new package, and a couple of its dependencies (#9920)
* r-geor: new package, and a couple of its dependencies

* Update to new copyright header

* Include the list_url for the R package archive dir

* Added explicit version ranges on dependencies, as per the relevant CRAN pages

* Correct dependency types in r-splancs.
2018-11-24 14:21:54 -06:00
Andreas Baumbach
862d1799fb new version 18.1 for py-pip (#9938)
Change-Id: Ie462e802049dd6150767dc555fb5708999e081ec
2018-11-23 18:09:20 -06:00
Neil Flood
2e510413c3 r-compositions: new package, including its dependencies (#9921)
* r-compositions: new package, including its dependencies

* Include the list_url for the R package archive dir

* Added explicit version ranges on dependencies, as per the relevant CRAN pages
2018-11-23 18:06:57 -06:00
Neil Flood
3557b6e149 libspatialite: new package (#9923) 2018-11-22 13:54:52 -06:00