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7588 commits

Author SHA1 Message Date
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
Michael Kuhn
c717f56359 ncl: Add 6.6.2 (#10800) 2019-03-05 17:13:51 +01:00
Michael Kuhn
21fb7dadb3 openssl: Add 1.1.1b, 1.1.0j and 1.0.2r (#10779) 2019-03-05 16:26:18 +01:00
Matthias Diener
9ba4d4e2af git-lfs: add version 2.7.1 (#10770) 2019-03-05 16:25:20 +01:00
Greg Sjaardema
d580d2a033 seacas: Update NetCDF version requirement (#10787) 
Modified NetCDF requirement to allow NetCDF-4.6.2 and subsequent versions.
 2019-03-05 14:05:52 +01:00
Justin Stanley
f19a214a19 libbeagle: add 3.1.2 (#10789) 2019-03-05 14:02:52 +01:00
Peter Scheibel
af4a36c4d9
Header subdirectories for Python and Eigen (#10773) 
Fixes #10769 

This updates the .headers property to include header subdirectories
for Python and Eigen (as is recommended by these packages).

#10623 updated the default behavior of .headers.directories to
exclude subdirectories (since this can cause clashes with system
headers). This broke some packages which depended on the old behavior
of .headers.directories: for example if you had
<package-prefix>/include/subdir/ex1.h, .headers.directories would
include <package-prefix>/include/subdir.
 2019-03-04 12:36:51 -06:00
Brian Van Essen
0ce1500376 Package Updates for ECP CANDLE Supervisor (#10760) 
* Add EQ-R package
* Add Fansi, Pillar, UTF8 (R) packages
* Add new versions for py-mdanalysis, r-cli, r-dplyr, r-pkgconfig,
  r-rlang, r-tibble, stc, and turbine packages
* Add hdf5 support for turbine
* Specify configure directory for stc package
 2019-03-01 14:46:13 -06:00
Justin Stanley
c8557ba7d8 blast2go: new package at 5.2.5 (#10725) 
* blast2go: new package at 5.2.5

* blast2go: remove redundant url
 2019-03-01 12:36:00 -06:00
Matthias Diener
ee5e5ce3c6 new package: intel-pin (#10546) 2019-03-01 12:29:01 -06:00
Justin Stanley
1a8161a982 r-bfastspatial: new package at 0.6.2 (#10734) 2019-03-01 10:18:14 -06:00
Justin Stanley
cbc6a2070a r-bfast: new package at 1.5.7 (#10733) 2019-03-01 10:17:37 -06:00
Justin Stanley
94357a274c bedops: avoid static linking with glibc (#10456) 2019-03-01 10:17:01 -06:00
Justin Stanley
165d8da0c2 blast-legacy: new package at 2.2.26 (#10610) 
* blast-legacy: new package at 2.2.26

* blast-legacy: compile from source

* blast-legacy: add missing os.symlink import

* blast-legacy: fix build script interpreter
 2019-03-01 10:14:37 -06:00
Justin Stanley
f9947333ca bridger: new package at 2014-12-01 (#10611) 2019-03-01 10:09:23 -06:00
Justin Stanley
c4aba6a204 r-spatial: new package at 7.3-11 (#10728) 2019-03-01 09:57:59 -06:00
Justin Stanley
16af5f31d9 r-nortest: new package at 1.0-4 (#10729) 2019-03-01 09:55:30 -06:00
Justin Stanley
4f1044a072 r-xts: add 0.11-2 (#10730) 2019-03-01 09:54:26 -06:00
Justin Stanley
104a8a1422 r-gdalutils: new package at 2.0.1.14 (#10731) 2019-03-01 09:53:30 -06:00
Justin Stanley
0766e7fbbb r-rgdal: add 1.3-9 (#10732) 2019-03-01 09:52:07 -06:00
Justin Stanley
89f59f7ab0 hyphy: new package at 2.3.14 (#10759) 2019-03-01 09:31:46 -06:00
Jiawei Zhuang
433cc4a972 Fix sha256 sum for IOR (#10765) 2019-03-01 09:59:36 +01:00
Sajid Ali
6d20e938da petsc: add +knl variant 2019-02-28 11:07:04 -06:00
Satish Balay
f8da8dbd0e
Trilinos: add release 12.14.1 (#10740) 
xsdk: switch from 12.14.0-rc1 to 12.14.1
 2019-02-28 11:05:05 -06:00
Eric Martin
4e80977506 py-tetoolkit: Add version 2.0.3 (#10749) 2019-02-28 12:59:30 +01:00
Owen Solberg
fac2dbda07 git-lfs: patch Makefile for v2.7.0 (#10720) 
Fixes #10702

Same fix merged upstream in git-lfs/git-lfs#3545 -- it may appear
in future release v2.7.2 according to package maintainer.
 2019-02-27 16:02:25 -06:00
Justin Stanley
2f4f828b45 wtdbg2: new package (#10639) 
* wtdbg2: new package at 2.3

* wtdbg2: flake8 fix
 2019-02-27 13:27:45 -06:00
Michael Kuhn
b1a04b7699 mpich: Improve package (#10643) 
- Add missing pkg-config, libpciaccess and libxml2 dependencies
- Add slurm variant for nodelist parsing
- Add missing configure flag for libfabric
- Unset F90 and F90FLAGS
- Allow selecting different PMI interfaces
 2019-02-27 13:13:44 -06:00
Paschalis Korosoglou
ab499a958d otf2 package: fix download URL (#10735) 2019-02-27 12:47:56 -06:00
Gregory Lee
d60106a3f6 Add newer versions for 51 Python packages (#10738) 2019-02-27 12:45:28 -06:00
Massimiliano Culpo
7eec038690
Update environment-modules package (#10717) 
The environment modules package has been updated to include 
versions up to 4.0.0. The url of the package and the homepage
have been updated accordingly.

The `spack bootstrap` command now builds version 3.2.10 of
the environment-modules package, and will do until #10708 
is fixed.
 2019-02-27 14:00:46 +01:00
Isaac Whitfield
5efff5d2fc new package: libusb (#10682) 2019-02-26 20:52:47 -06:00
Isaac Whitfield
938939b7e4 new package: libtasn1 (#10681) 2019-02-26 20:52:04 -06:00
Nichols A. Romero
d9b7c1faea QMCPACK package: cuda/hdf5 fixes (#10701) 
* Make use of new QE multi-valued HDF5 variant interface
* Remove explicit CUDA dependency (which is handled by inheriting
  from CudaPackage)
* Update cuda_arch unset variant check
 2019-02-26 20:50:32 -06:00
Satish Balay
c11f598e0b petsc: add version 3.10.4 (#10724) 2019-02-26 20:41:33 -06:00
Justin Stanley
cbecf9f555 new package: phred (#10700) 
Part of the software collection introduced in #10529. Developers must
be contacted via email to receive the source code.
 2019-02-26 19:14:58 -06:00
Isaac Whitfield
fbdbed1180 new package: libplist (#10680) 
Dependency of Google's Flutter toolchain.
 2019-02-26 19:12:41 -06:00
Justin Stanley
df4b77f120 libbeagle package: add cuda support (#10650) 
libbeagle compiles against CUDA by default but no there is no mention
of it in the package recipe. This PR adds explicit cuda paths and
variants, and fixes the target architecture as well (for those who
don't have compute_13)
 2019-02-26 18:50:08 -06:00
Michael Kuhn
0adf1b5405 vampirtrace: patch for new mpich and openmpi versions (#10665) 2019-02-26 18:48:14 -06:00