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7626 commits

Author SHA1 Message Date
Greg Sjaardema
204063e21a cgns package: add version 3.4.0 and update hdf5 dependency (#10803) 
* Add version 3.4.0
* Update checksums for older versions to sha256
* Require hdf5~mpi when building with ~mpi
 2019-03-11 19:43:16 -05:00
Eric Martin
dc0b6a0613 samtools package: Add version 1.5 and htslib 1.5 dependency (#10825) 2019-03-11 19:29:29 -05:00
Alberto Chiusole
2b591653fa hdf5 package: add version 1.10.5 (#10794) 2019-03-11 15:15:03 -05:00
Justin Stanley
46466381b8 py-crossmap: new package at 0.3.3 (#10854) 2019-03-11 15:13:02 -05:00
Michael Kuhn
9425075a23 flex: Apply 2.6.4 patch regardless of gcc version (#10841) 
It seems that this is actually a glibc problem and while 2.6.4 builds
without the patch on newer versions of gcc (@8:), it still sometimes
segfaults (as observed during the doxygen build).
 2019-03-11 15:12:28 -05:00
Ce Qin
43525d3445 mpich: remove libpciaccess dependency for MacOS (#10795) 2019-03-11 15:06:49 -05:00
Gregory Lee
1fd01af773
added intel 19.0.3 packages (#10835) 
* added intel 19.0.3 packages

* added intel 19.0.3 packages
 2019-03-11 07:03:24 -07:00
Chris Green
1931bc8b40
Add 2019.{3,4} and patches for pedantic warnings. (#10836) 2019-03-11 09:03:19 -05:00
Chris Green
7e22fdfa21
boost: patch for problem with warnings for 1.69.0. (#10820) 2019-03-11 09:02:50 -05:00
Eric Martin
43b45f4140 breseq package: Add version 0.33.2 and zlib dependency (#10747) 
For zlib, also update the `CFLAGS`/`LDFLAGS`
 2019-03-08 20:57:00 -06:00
Denis Davydov
c81e68030a intel: add 2019.3 (#10843) 2019-03-08 14:50:58 -08:00
Christoph Junghans
0d07dea2eb
snap: overwrite flags (#10832) 2019-03-07 14:53:04 -07:00
Christoph Junghans
c11e745421
cloverleaf3d: overwrite flags (#10830) 2019-03-07 14:08:52 -07:00
Christoph Junghans
2f7589adc4
cloverleaf: overwrite flags (#10829) 2019-03-07 14:08:36 -07:00
Levi Baber
016945f67a
autofact: fix dependency (#10818) 2019-03-07 13:51:40 -06:00
Eric Martin
e750c5af66 trimmomatic package: restrict java dependency to version 8 (#10741) 2019-03-07 13:49:57 -06:00
Tristan Carel
dd6e91fcb6 Nix package: update dependencies (#10646) 
* Add 'fiber' as a default library for boost
* Add autoconf/automake etc. dependencies to libseccomp package
* New package: brotli
* New package: editline
* Add brotli, editline, boost dependencies to Nix
 2019-03-07 13:32:55 -06:00
Matthias Maiterth
23822e9717 GEOPM package: add version 1.0.0-rc2 (#10737) 2019-03-07 13:18:05 -06:00
Eric Martin
d072a1e0e3 py-sip package: Add version 4.19.3 (#10742) 2019-03-07 13:16:54 -06:00
Eric Martin
435db9d1a5 seqtk package: Add version 1.3 (#10743) 2019-03-07 13:16:20 -06:00
Michael Kuhn
3fb75e1206 flex package: patch for building 2.6.4 with gcc 7 (#10754) 
Remove 2.6.3 as preferred version (but keep it available for
building). The latest version (currently 2.6.4) is now preferred
(according to Spack's defaults).
 2019-03-07 13:15:47 -06:00
Eric Martin
49e307398b py-certifi: Add version 2017.4.17 (#10828) 2019-03-07 13:09:26 -06:00
Michael Kuhn
2fed84058d py-flake8: Add missing dependencies for @3.7.7 (#10796) 
* Update dependencies for py-flake8 when building version 3.7.7
* Add FIXME comment for an example dependency constraint which causes
  concretization to hang
* Add py-entrypoints version 0.3
* Add py-pycodestyle version 2.5.0
 2019-03-07 12:50:30 -06:00
健美猞猁
42633e34ab CMake package: update libuv dependency constraints (#10824) 
* Add libuv version 1.10.0
* CMake versions before 3.12.0 do not build with libuv version
  1.25.0, so a constraint is added to build earlier versions of
  CMake with libuv version 1.10.x
 2019-03-07 12:42:24 -06:00
prs513rosewood
32bbffc869 thrust: add versions 1.9.0-1.9.4 (#10823) 2019-03-07 14:36:59 +01:00
Eric Martin
efdeb860d1 transdecoder package: Add version 5.5.0 and fix up url and installation paths (#10745) 
* Add version 5.5.0 and fix installation locations
* URL format has changed as of version 5.5.0
* Update paths created for installation
 2019-03-06 20:58:50 -06:00
Eric Martin
45856c3660 bsseeker2 package: Add versions 2.1.8 and 2.1.5 (#10748) 
As of version 2.1.8, the url format changed, so also update that
 2019-03-06 20:55:06 -06:00
Jeongseok Lee
0e22a94f81 Eigen package: support Spack-external builds using Eigen (#10751) 
Update CPATH in setup_environment for Eigen, so that the
Spack-generated module for Eigen will help builds outside of Spack
use the appropriate include prefix for Eigen headers 
(<install_prefix>/include/eigen3/ rather than <install_prefix>/include/)
Note that this only updates the run-time environment, rather than the
build-time environment, so Spack builds depending on Eigen that use
pkgconfig will not be confused by the presence of the Eigen include
directory in CPATH.
 2019-03-06 20:48:38 -06:00
Matthias Diener
836f40e30f scons: add version 3.0.4, cleanup URLs (#10806) 2019-03-06 20:39:39 -06:00
HAOCHENG LIU
a3a8ed7234 vtk-m package: turn off mpi support by default (#10755) 2019-03-06 20:34:49 -06:00
健美猞猁
9d880b8838 New package: dysco (#10767) 2019-03-06 20:25:06 -06:00
Greg Sjaardema
c19df8be5d NetCDF package: update constraints on hdf5 mpi support (#10788) 
Update NetCDF to require building hdf5 without mpi when NetCDF itself
is built without mpi support.
 2019-03-06 20:20:16 -06:00
Satish Balay
35daaa440f omega-h: add version 9.22.2 and update gcc 8 conflict (#10776) 
* Versions before 9.22.2 compiler with gcc 8.3 or later
* Added version 9.22.2, which compiles with all gcc 8.x versions
  (including those before 8.3)
 2019-03-06 20:10:47 -06:00
Ryan S. Elliott
39467e4d67 Update kim-api package and add openkim-models-v2 (#10780) 
* Replace kim-api package with kim-api-v2, which has different
  versions and removes the 'cmake_args' method
* Add openkim-models-v2 as an extension package
 2019-03-06 19:23:05 -06:00
Mark W. Krentel
edecdc3ace libelf: move url to fossies.org (#10815) 
* libelf: move url to fossies.org

Libelf is no longer maintained and the original mr511.de web site no
longer exists.  The final release, 0.8.13 from Nov 2009 is still
archived at fossies.org.

Fixes #10757.

* Change the homepage to the FSF entry.
 2019-03-06 11:42:44 -08:00
Gregory Lee
10b0251af0 added python 2.7.16 (#10805) 2019-03-06 11:05:32 -08:00
Gregory Lee
86a1230a60 build fixes for util-linux (#10811) 2019-03-06 11:04:53 -08:00
Cameron Stanavige
9f734e0cfd unifycr: dependency changes and new version (#10722) 
New release of UnifyCR. Remove unsupported pre-1.0 versions

UnifyCR has had a few dependency changes to make the backend more
efficient. A new pre-release version has been released as well to
mark these changes. Prior versions are no longer supported.
 2019-03-06 10:56:20 -08:00
Owen Solberg
ff7cd40ca1 update package rsem (#10813) 2019-03-06 14:57:54 +01:00
Isaac Whitfield
1605368148 libusbmuxd: new package (#10726) 2019-03-06 10:10:02 +01:00
健美猞猁
c5573e660c intel-parallel-studio package: add version cluster.2019.2 (#10782) 2019-03-05 18:08:00 -06:00
健美猞猁
40d66e34d3 New package: pal (#10766) 2019-03-05 17:41:54 -06:00
健美猞猁
063f5b63da New package: erfa (#10763) 2019-03-05 17:40:39 -06:00
Greg Sjaardema
4c493b065c NetCDF package: add version 4.6.3 and update naming (#10786) 
* Add NetCDF version 4.6.3
* Naming scheme for artifacts >= 4.6.2 has changed. Add a
  url_for_version function to generate the appropriate URLs
 2019-03-05 17:33:47 -06:00
clellsolomon
b72715ed7c Add fzf utility package (#10778) 
* Add fzf utility package

* Fix "style checks" errors

- var/spack/repos/builtin/packages/fzf/package.py:32:
  [E226] missing whitespace around arithmetic operator
 2019-03-05 17:17:48 -06:00
Michael Kuhn
5758e49c80 gcc package: Add 8.3.0 (#10772) 2019-03-05 17:15:57 -06:00
Gregory Lee
7bd8689f06 openss package: allow all 2.7.x versions (#10807) 
Originally the version constraint range had an upper bound of 2.7.15
This allows all 2.7.x versions
 2019-03-05 17:14:32 -06:00
Alberto Chiusole
63e172d2ac RegCM: intel FC 'hint', 4.7.0 intel warning, fcflags, fix extensions. (#10797) 
This should fix and improve #9934, which was messed up by a fetch from develop
 2019-03-05 21:30:53 +01:00
Gregory Lee
bad485a221 various package version updates and build fixes (#10775) 
* various package version updates and build fixes
 2019-03-05 11:59:47 -08:00
Matthias Diener
c939e36ed9 cantera: make sundials dependency optional (#10764) 2019-03-05 19:58:00 +01:00