Commit graph

10552 commits

Author SHA1 Message Date
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
Nicholas Labello
13f2e68688 munge: update versions and url format to reflect switch to .xz format… (#9916)
* munge: update versions and url format to reflect switch to .xz format in recent releases

* package:munge remove unneeded version-specific urls
2018-11-22 13:13:40 -06:00
Eric
be92d46962 minced: add version 0.3.2 and fix install paths (#9918) 2018-11-22 13:13:06 -06:00
Neil Flood
c42ceb886c qca: new package (#9924) 2018-11-22 12:45:42 -06:00
Neil Flood
b6e664846a qjson: new package (#9925) 2018-11-22 12:45:17 -06:00
Denis Davydov
0f6f3ece95 p4est: apply patches to 2.0 only (#9928) 2018-11-22 12:40:22 -06:00
Michael Kuhn
f7a445e4b0 multitime: new package (#9929) 2018-11-22 12:39:51 -06:00
Michael Kuhn
ffaf617e74 flecsale: add missing dependencies and fix flecsi runtime model (#9774) 2018-11-22 12:38:59 -06:00
Ken Raffenetti
0eb8cd9a8f Add MPICH version 3.3 (#9915) 2018-11-21 14:42:52 -06:00
Mark W. Krentel
27ad0f1269 dyninst: overhaul package.py to CMakePackage (#9871)
Drop versions 8.1.x.  These were > 5 years old, no other spack package
uses them, and they used autotools.  Packages 'stat' and 'mitos' still
use 8.2.1, so we keep that.

Switch class Dyninst to CMakePackage.

Clean up how the versions depend on various packages.  For example,
Dyninst used libelf up to 9.2, and then elfutils starting with 9.3.
This makes things easier going forward.

Add variant 'openmp' (default True) to enable openmp support for
ParseAPI.  This was added in 10.0.0.

Add variant 'static' (default False) to also build static libraries.
This goes back to 9.1.0.

Disable cotire for the 9.3.x versions.  Cotire has no real use in a
one-time build and can break parallel builds with both static and
shared libs.
2018-11-21 10:47:19 -08:00
Elsa Gonsiorowski, PhD
1c5688fcbc correct sha for axl v1.1 (#9907) 2018-11-20 19:28:47 -06:00
Tom Scogland
ba5a251896 package: add asciidoctor gem (#9905)
* package: add asciidoctor gem

Faster, easier to use, less impossible to install correctly
implementation of asciidoc.

* ritual sacrifice of EOF whitespace to flake8
2018-11-20 14:32:44 -06:00
Tiziano Müller
84bc1d6654 CP2K related fixes and update (#9308)
* openblas: enable parallel builds

* cp2k: enable parallel builds

* cp2k: fix building on multilib/Suse distros

use the actual directory path where files where installed to instead of
the default prefix+'/lib'

* cp2k: ensure we have a non-header-only libxsmm

* openblas: disable max num CPU detection on virtualized build

* cp2k: install data and set compiled-in DATA_DIR

* cp2k: make libxc an optional dependency (enabled by default)

* cp2k: link libint statically

* cp2k: declare statically linked library deps as type=build

* cp2k: add support for PGI compiler

* cp2k: rename smm=none to smm=blas for clarification

* cp2k: blacklist unsupported compilers

* cp2k: mark wannier90 a build-time dep since statically linked

* cp2k: make pexsi and elpa optional

* cp2k: add support for v6.1

* libxc: add version 4.2.3

* cp2k: use pkg-config to link properly to libxsmm

* cp2k: fix OpenMP support by making it explicit

Previously, CP2K accepted threaded ELPA or BLAS, leading to #(CPU) processes
being spawned even though no explicit OpenMP was requested. Now the
`popt` variant should truly be thread free while the `psmp` variant uses
threads also internally.

* cp2k: source tarballs moved to GitHub
2018-11-20 09:23:01 -08:00
dorier
13b95b8ae6 Package: Mercury (#9903)
* added mercury package

* updating mercury package to satisfy flake8

* improved mercury package
2018-11-20 11:14:30 -06:00
Jon Rood
128af27c21 Add 2019.1 and 2018.4 version of the Intel performance libraries. (#9899)
* Add 2019.1 and 2018.4 version of the Intel performance libraries.

* Fixing typo.
2018-11-20 09:30:53 -06:00
Adam Moody
5127bb590f mpifileutils: add v0.8.1 (#9346) 2018-11-19 20:48:50 -06:00
Michael Kuhn
44d1d928e8 openssl: make 1.1.1 the default version (#9836)
* openssl: add 1.0.2p, 1.1.0i and 1.1.1

* openssl: make 1.1.1 the default version
2018-11-19 20:46:38 -06:00
Justin Stanley
7bb9020227 added several new perl modules (#9760) 2018-11-19 20:44:44 -06:00
Justin Stanley
9dfea8ee17 circos: new package starting at 0.69-6 (#9761)
* circos: new package starting at 0.69-6

* circos: add homepage, simplify paths

* circos: simplified more paths
2018-11-19 20:44:01 -06:00
Sinan
0a0e5642df gdk-pixbuf: explicitly disable building of gtk-docs (#9882) 2018-11-19 20:42:56 -06:00