Commit graph

11473 commits

Author SHA1 Message Date
Massimiliano Culpo
bdb5d17eb8 yambo: added versions 4.2.2 (#8298) 2018-05-28 08:01:29 -05:00
Adam J. Stewart
5490190b71
Add JasPer 2.0.14 (#8207)
* Add JasPer 2.0.14

* Remove no longer necessary patch

* Explicitly disable generation of documentation

* Re-add support for JasPer 1.900.1, add GDAL patch

* Remove GDAL patch
2018-05-26 10:37:48 -05:00
Adam J. Stewart
1549ee76e5
Add GDAL 2.3.0 (#8263)
* Add GDAL 2.3.0

* Add missing dependencies, change default variants, and add links

* GDAL requires old hacked version of JasPer

* Move JasPer patch to GDAL
2018-05-26 10:37:22 -05:00
Adam J. Stewart
7602fcd4d0
Fix compilation of FYBA with GCC 6 (#8273) 2018-05-26 10:36:34 -05:00
Elizabeth Fischer
8203c4f55b Fix gettext: Problem with libxml2 (#8132)
* See https://github.com/spack/spack/issues/2882

* code review

* Correctly access lib directory
2018-05-26 10:18:14 -05:00
Corey McNeish
7a741e7e08 Fix OpenCV JasPer disable (#8287)
The recipe previously did not include -DWITH_JASPER
Other edits:
 * BUILD_IPP_IW is BUILD instead of WITH; it was in a different section of the CMakeLists.txt. Move it to the top
 * Several options were missing :BOOL, add them
 * -DWITH_ZLIB doesn't actually exist as an option, at least in the latest version.
2018-05-26 00:44:18 -05:00
Nate Roberts
90d1478f50 Added new package Camellia. (#8190)
* Added new package Camellia.

* Fixed an issue with a missing blank line.

Added a couple more Trilinos packages (things I expect to depend on eventually).

* Fixed a couple issues raised by @adamjstewart.

* Specified 4.9.2 as the supported MOAB version.

5.0.0 causes build issues on Macs during the link of Camellia's drivers.  The issue is that we end up with -framework -lAccelerate in the link line, where it should read -framework Accelerate, I believe.  I'm not sure where this comes from, but 4.9.2 does not have this issue.

* Trimmed slightly the Trilinos requirements.

Also deleted a blank line that had spaces in it because the Travis-CI thing didn't like that.

* Reduced length of MOAB description (Travis-CI complained).

* Reduced the MOAB line further; didn't quite get there last time!

This is to satisfy Travis-CI's requirement that the description be less than 80 characters long (E501).

* Put in my GitHub handle, in place of an allusion to my email address.

Also added a new argument for Camellia build, and made the MOAB description longer (thanks to @adamjstewart's note that long lines are allowed so long as they are not split).

* Added MPI dependency.

Added explicit OFF for MOAB enablement when ~moab.

Swapped order of variant and version.
2018-05-25 23:06:05 -05:00
Levi Baber
1c2dc8f528 repeatmasker: fix bin location and dependency (#8286) 2018-05-25 18:22:25 -05:00
Andrey Prokopenko
3c10d160d0 flang: add non-develop version (#8276) 2018-05-25 14:01:19 -05:00
Levi Baber
6899c9e6c3 perl-text-soundex: new package (#8279)
* perl-text-soundex: new package

* perl-text-soundex: formatting
2018-05-25 14:00:12 -05:00
David Guibert
468570114f hdf5: add 1.10.2 (#8274) 2018-05-25 09:06:50 -05:00
George Hartzell
28e7248b06 Add Tophat v2.1.2, fixes automake issues (#8266)
* Add Tophat v2.1.2, fixes automake issues

The Tophat team merged the patch from
https://github.com/spack/spack/pull/8244 and release v2.1.2

This change requires the old automake if you're building the older
release and is relaxed about the automake it requires if you're
building the v2.1.2 release.

Building v2.1.1 and v2.1.2 works on a CentOS 7 system, I don't have
the necessary bit to actually test the resulting binaries.

Here's the commit note from the change that was ultimately merged
upstream.

Fixes #8025

> Tophat was failing to build with automake@1.16.1, it worked with the
> older automake@1.15.1. This commit adds a patch to Tophat's
> src/Makefile.am which cleans up a few things. The result builds
> successfully with both automake@1.15.1 and automake@1.16.1. I have no
> way to check that the resulting builds Do The Right Thing.
>
> It changes two things:
>
> the original Makefile.am had a rule for $(SAMPROG) with no
> actions, and since there was a directory there with a tempting name
> the newer automake was trying to do something with it, but lacked
> the appropriate clues. Since that target is actually made as a side
> effect of making the library (sigh...), it seems to work to just
> give that rule something harmless to do (the Peter Principle
> triumphs again...).
>
> a bunch of the targets need a libtophat.a and libgc.a; the older
> automake was probably able to guess what to do given the list of
> sources but the newer automake apparently won't make the necessary
> assumptions. This patch wires up a simple rule and cleans up the
> appropriate dependencies so that things work.
>
> While it may appear that I'm someone who understands automake, keep in
> mind that I only play such a person on a TV reality show. YMMV.

* Remove extraneous when constraint
2018-05-24 20:04:03 -05:00
Luca Heltai
c25759e1c8 Added gsl dependency to pnfft (#8255) 2018-05-24 16:24:47 -05:00
Michael Kuhn
c77bc613eb Fix missing spack.compiler import (#8240)
Fixes: #8258

#8090 altered import behavior so that import spack no longer
provides access to many other Spack modules. This addresses
a case which depended on the prior behavior and was not
updated as part of #8090. This particular import error only
came up when users were setting compiler flags on specs.

See also: #8194
2018-05-24 10:59:20 -07:00
Geoff Womeldorff
fdb2d6f493 kokkos: update kokkos spackage to add current host/gpu architectures. (#8226)
* kokkos: update kokkos spackage to add current host/gpu architectures.

* kokkos: simplify host/gpu architecture selection and make intent of arg population logic more clear.

* kokkos: mollify flake8.

* Make strings and logic more pythonic. Add error for GPU arch without CUDA.

* kokkos: simplify conflicts behaviour. make args population more pythonic.

* kokkos: move gpu values to list for use in variant and conflicts checking.

* kokkos: How fortunate the man with None.

* kokkos: fix gpu_arch conflict loop error. add conflict to guard against +cuda and 2.5.00:develop versions, until kokkos issue #1296 is resolved.

* kokkos: mollify flake8.

* kokkos: add descriptive message to version conflict with +cuda.
2018-05-24 10:53:58 -05:00
Matthias Diener
4c4e2866d8 Charm++: Add possibility to build git version (#8260) 2018-05-24 10:48:37 -05:00
Sajid Ali
5fff4da5b7 Add msgpack-c 3.0.1 (#8264)
* 	new file:   cpp-3.0.1.tar.gz
	modified:   package.py

* 	deleted:    cpp-3.0.1.tar.gz

* remove whitespace
2018-05-24 10:47:31 -05:00
Levi Baber
fdf889264e trf: make executable (#8265) 2018-05-24 10:47:17 -05:00
Chris Hadjigeorgiou
db4062b01f openfoam-org: add v2.4.0 (#7850)
Add 2.4.0 changes
2018-05-24 08:44:41 -07:00
jkelling
fa1153d116 Fix MD5 hash for opencv 3.2.0 and 3.1.0 release (#8241) 2018-05-24 08:59:11 -05:00
George Hartzell
80e4c7da0e Add info for datamash@1.3 (#8261) 2018-05-23 18:40:14 -05:00
Adam J. Stewart
9b9980256f
Add kealib 1.4.7 (#8235)
* Add kealib 1.4.7

* Fix out-of-source builds

* Remove username from kealib hg clone
2018-05-23 18:36:12 -05:00
Adam J. Stewart
8f3d717a30
Add PROJ 5.0.1 (#8233)
* Add PROJ 5.0.1

* proj-datumgrid resource must be placed in nad directory
2018-05-23 13:29:08 -05:00
Massimiliano Culpo
0ea8c4f3b2 mvapich2: added a proper libs attribute (#8253) 2018-05-23 13:28:21 -05:00
Adam J. Stewart
13a1575452
Add pkgconf 1.4.2 (#8256) 2018-05-23 13:27:39 -05:00
Adam J. Stewart
f57ce38c41
Add ncurses 6.1 (#8257) 2018-05-23 13:27:22 -05:00
Edward Kim
011d1245fb charm: Update install script (#7291)
* charm: Update install script

* Addressed PR comments

* Removed destination and suffix variants

* Added back parallel support
2018-05-23 13:26:59 -05:00
Massimiliano Culpo
9fee111741 gromacs: added version 2018.1 (#8251) 2018-05-23 10:13:09 -05:00
Massimiliano Culpo
251019c5e4 cgal: added version 4.12 (#8252) 2018-05-23 10:11:03 -05:00
Tim Law
60df206648 Update BookLeaf_Cpp and Typhon packages. (#8249) 2018-05-23 07:28:15 -05:00
Leonhard Reichenbach
ace283d594 Add latest versions of bazel (#8250) 2018-05-23 07:27:45 -05:00
Sinan
bc73e85af8 Package/mirdeep/fix for new url take2 (#8247)
* rename: mirdeep -> mirdeep2

* fixes for new url
2018-05-23 07:25:42 -05:00
Leonhard Reichenbach
3712ac1f66 Create new package: memkind (#8242)
* Create new package: memkind

* some style changes

* fix type of numactl dependency

* fix flake8 errors

* use patch() instead of a custom build phase
2018-05-22 13:37:03 -05:00
Adam J. Stewart
4d3ed1ff13
Add py-docopt package (#8236) 2018-05-22 10:49:12 -05:00
Massimiliano Culpo
0106c6cab7
subread: added version 1.6.2 (#8239) 2018-05-22 14:16:06 +02:00
Axel Huebl
cd72312940 CUDA 9.2 (#8238)
Add the latest CUDA release, v9.2 and updated CUDA Compatibility Matrix
2018-05-22 12:45:47 +02:00
Tim Stavenger
b61175aeba Update GlobalArrays package to new releases (#7840)
* update globalarrays package to current releases

* rename class to Globalarrays to match package folder

* rename bytes to int64, minor cleanup of descriptions

* int64 False by default

* remove reference to external as we aren't supplying paths, and use args.append()

* correcting args.append syntax

* add conflicts
2018-05-21 20:06:29 -05:00
Elizabeth Fischer
68e7fd053e gdbm: Get working on CentOS5 and Other Older Systems (#8134)
* Fix #7691

* flake8

* code review
2018-05-21 16:24:38 -05:00
Elizabeth Fischer
90d36016ef netcdf-cxx4: Update to use CPPFLAGS (#8148)
* Fix bug; don't know why this ever worked in the first place.

* Add fix to netcdf-fortran too; flake8

* Simplify configure_args()

* netcdf-fortran: simplify that too
2018-05-21 16:23:35 -05:00
lingnanyuan
646771300d Create new package: fastgbs and its dependency platypus. (#8174)
* pushing partially done recipe for fast-gbs and platypus

* modify platypus

* change header

* fast-gbs: change dependency type.

* modify dependency type.

* modify dependency type.

* fast-gbs: Change dependency type to run.
2018-05-21 16:13:05 -05:00
peetsv
2cfde03a60 r-cghflasso v0 2 1 - new package (#8177)
* py-pyfaidx: adding new package

* updating the url

* r-cghflasso v0.2-1 new package

* correcting copy/paste error

* adding list_url
2018-05-21 16:12:35 -05:00
Jim Galarowicz
d7aaf4e193 Add urls into cbtf* and openspeedshop* package files and update the release versions for the Krell products (#8188) 2018-05-21 16:03:31 -05:00
Dan FitzGerald
8564be5479 Rename Tpetra C wrappers for *gemm Fortran functions in Trilinos 12.12.1 (#8228)
* Updated trilinos to compile/install with xl_r

* Undo PGI patch added as part of Trilinos XL fix

* Remove PGI related changes in Trilinos XL fix
2018-05-21 16:00:10 -05:00
Adam J. Stewart
fba365dc6a
Add Python/Ruby bindings to GEOS package (#8218)
* Add python/ruby bindings to GEOS package

* Add comment on Python 3 support
2018-05-21 15:59:50 -05:00
Adam J. Stewart
ac2b0f3ac0
Add lcms 2.9 (#8219) 2018-05-21 15:59:11 -05:00
Adam J. Stewart
ed0f5e9b4c
Add missing dependencies to poppler package (#8220) 2018-05-21 15:58:51 -05:00
Adam J. Stewart
729c3f9168
Add bmake 20180512 (#8221)
* Add bmake 20180512

* Re-add manpage patch
2018-05-21 15:58:11 -05:00
Eric
6ec603860a py-testinfra: Add versions 1.12.0 and 1.13.0 (#8222) 2018-05-21 15:57:25 -05:00
George Hartzell
e954686e5a Add info about haveged to gpg/randomness note (#8227) 2018-05-21 15:57:03 -05:00
mcneish1
15634c20fe Update the hash of libjpeg v9c. (#8230)
The maintainer redid the archive in March, removing a .directory file.
2018-05-21 15:53:55 -05:00