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10213 Commits

Author SHA1 Message Date
iarspider
7d96e496b2
Add extra version of jemalloc (#14955) 2020-02-15 23:08:37 -06:00
iarspider
e75b8c1230
Add extra version of json-c (#14956) 2020-02-15 23:08:13 -06:00
iarspider
41a2a5db2c
Add extra version of libgit2 (#14957) 2020-02-15 23:07:38 -06:00
iarspider
8f877fdc65
Add extra version of libsodium (#14958) 2020-02-15 23:07:12 -06:00
iarspider
bab407a28a
Add extra version of libsvm (#14959) 2020-02-15 23:06:48 -06:00
iarspider
8308d2d59d
Add extra version of libxkbcommon (#14961) 2020-02-15 23:06:17 -06:00
iarspider
a6dc3fe40b
Add extra version of nlohmann-json (#14962) 2020-02-15 23:05:54 -06:00
iarspider
12ec8e340f
Add extra version of pcre (#14963) 2020-02-15 23:05:30 -06:00
iarspider
f547f2ce10
Add extra version of pixman (#14964) 2020-02-15 23:05:09 -06:00
iarspider
00de09268e
Add extra version of py-absl-py (#14965) 2020-02-15 23:04:40 -06:00
iarspider
ee573540a0
Add extra version of py-asn1crypto (#14967) 2020-02-15 23:03:17 -06:00
iarspider
d7de6cf055
Add extra version of py-arrow (#14966) 2020-02-15 23:02:21 -06:00
iarspider
ad7c11c482
Add extra version of py-astroid (#14968) 2020-02-15 23:01:53 -06:00
iarspider
ff71844bf6
Add extra version of py-attrs (#14969) 2020-02-15 23:01:24 -06:00
Nichols A. Romero
98c4d15655
Flang - Support libomptarget offload to NVidia GPU (#15015) 
* Modify Flang NVidia GPU variant to make use of built-in CudaPackage

* Add OpenMP Offload patch if March 2019 compiler is selected.

* Flang parallel build has a race condition.

* llvm-flang now uses built-in CudaPackage.

* Add variant for different build releases.

* Fix OpenMP target offload for NVidia GPUs.

* Additional commong flags that are needed with comments.

* NVidia BC required for libomp target requires special treatment. Use clang built in previous step to re-compile libomptarget.
 2020-02-15 22:56:58 -06:00
iarspider
4f3287a9dc
Add extra version of py-cython (#14974) 2020-02-15 22:52:36 -06:00
iarspider
45ee708596
Add extra version of py-coverage (#14976) 2020-02-15 22:48:10 -06:00
iarspider
959d9d2365
Add extra version of py-certifi (#14977) 2020-02-15 22:47:28 -06:00
iarspider
7c88bb937d
Add extra version of py-backports-abc (#14978) 2020-02-15 22:47:05 -06:00
iarspider
c92201e6ab
Add extra version of py-decorator (#14980) 2020-02-15 22:44:28 -06:00
iarspider
bcccf0d4e7
Add extra version of py-importlib-metadata (#14983) 2020-02-15 22:35:47 -06:00
iarspider
8313de5be0
Add extra version of py-ipaddress (#14984) 2020-02-15 22:35:23 -06:00
iarspider
4db0eb4917
Add extra version of py-ipykernel (#14985) 2020-02-15 22:33:04 -06:00
iarspider
8b5cc1e76f
Add extra version of py-ipython (#14986) 2020-02-15 22:32:28 -06:00
iarspider
bff3a087ec
Add extra version of py-jinja2 (#14989) 2020-02-15 22:27:53 -06:00
iarspider
bd24d53ceb
Add extra version of py-jpype1; add numpy as optional (variant) dependency (#14991) 
* Add extra version of py-jpype1

* Add numpy as optional (variant) dependency
 2020-02-15 22:24:44 -06:00
iarspider
2c0bfd071f
Add extra version of py-jupyter-client (#14996) 2020-02-15 22:21:48 -06:00
Glenn Johnson
e5e6791d97
package r-readbitmap Change jpeg dependency (#15004) 
This PR corrects the jpeg dependency in r-readbitmap to use the jpeg
virtual dependency.
 2020-02-15 21:50:54 -06:00
Justin S
4a7e4655ac
mafft: add 7.453 (#15006) 2020-02-15 21:48:26 -06:00
Matthias Diener
3f5d889d2b
cloc: add version 1.84 (#15012) 2020-02-15 21:34:11 -06:00
Keita Iwabuchi
b688bb549b
Add a new package: Metall (#14903) 
* Add a new package: Metall

* Fix errors in metall/package.py

* Update var/spack/repos/builtin/packages/metall/package.py

Change to https style URL

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update in metall/package.py. Change Metall to depend on Boost always

* Update in metall/package.py. Change to install Boost with the default variants

* Update metall/package.py. Removed a comment

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-02-15 00:34:32 -06:00
Scott Wittenburg
3c28e72d2f
cuda: add libxml2 as a dependency for newer versions (#14758) 2020-02-14 12:13:30 -06:00
Matthias Wolf
978a3bb7ef
py-whichcraft: new package (#14907) 
* py-whichcraft: new package

* address comment
 2020-02-14 08:00:58 -06:00
Sajid Ali
c607288a7c
fix env vars before install (#14575) 2020-02-13 20:16:34 -06:00
Brian Van Essen
d524abad20
Updated both cub and nccl versions. Fixed a bug in the cub download (#14852) 
url.
 2020-02-13 20:10:02 -06:00
Glenn Johnson
8beb42e749
New package: r-codex (#14869) 
This PR adds the r-codex package.

- new package: r-bsgenome-hsapiens-ucsc-hg19
 2020-02-13 20:00:39 -06:00
Kai Torben Ohlhus
4fa29ceb50
openblas: add variant +consistentFPCSR (#14876) 
Add the OpenBLAS variant `+consistentFPCSR`, by default `False`, which adds the compile definition `CONSISTENT_FPCSR=1` as documented in  OpenBLAS `Makefile.rule`.
 2020-02-13 19:59:34 -06:00
Dr. Christian Tacke
690ed2fe98
[rsync] Use popt and zlib (#14755) 
popt and zlib are available as spack packages.
So use them instead of building internal ones.
 2020-02-13 19:55:41 -06:00
Glenn Johnson
7996bc809a
New package: r-exomedepth (#14884) 
This PR adds the r-exomedepth package and r-aod as a dependency.
 2020-02-13 19:52:43 -06:00
Glenn Johnson
580c8f5b7e
New package: r-exomecopy (#14885) 2020-02-13 19:51:18 -06:00
Glenn Johnson
46ae3f0570
New package: r-fdb-infiniummethylation-hg18 (#14890) 
This PR adds the r-fdb-infiniummethylation-hg18 package and the needed
dependency of r-txdb-hsapiens-ucsc-hg18-knowngene.
 2020-02-13 19:49:24 -06:00
Glenn Johnson
725336ee48
Update and fix the r-rhtslib package (#14863) 
This PR adds an updated version to the r-rhtslib package as well as fix
the build.

- add patches to use compiler flags from R
- add variables for bzip2 and xz dependencies
- use the spack Makeconf file when building the in-tree htslib
- make patchelf available to allow R to remove reference to temporary
  installation directory in htslib shared object
- Add new version of r-rsamtools as the r-rsamtools and r-rhtlib
  packages are closely paired.
 2020-02-13 19:47:37 -06:00
Seth R. Johnson
0d0ab60150
Patch silo for %clang@9 (#14892) 2020-02-13 19:45:55 -06:00
Alec Thomas
9046deae80
Add missing dep to git. (#14895) 
As discussed in:
 https://spackpm.slack.com/archives/C5VL7V81G/p1581394270058800
 2020-02-13 19:45:09 -06:00
asmaahassan90
413de215b2
Fix run environment (#14908) 
* Fix run environment

Trying to install Avizo, i get "Error: NameError: name 'run_env' is not defined". Correcting it to be just "env"

* fix identation
 2020-02-13 19:37:39 -06:00
Mark W. Krentel
1c5f72dbaa
intel-tbb: update to new tar file names for 2020 versions (#14924) 
Starting with 2020, the tar files are named v2020.0.tar.gz,
v2020.1.tar.gz, etc, not 2020_U1.tar.gz.

https://github.com/intel/tbb/releases

The previous commit (7a10478708) fixed the checksum mismatch, but
didn't update url_for_version (my bad).
 2020-02-13 19:30:10 -06:00
Cameron Stanavige
4b7f057a4b
unifyfs: remove numa dependency (#14925) 
UnifyFS no longer has an option to depend on numa. This removes the
numa variant, dependency, and associated conflict.

This commit also

- renames the `pmpi` variant to the more appropriate `auto-mount`

- changes the preferred version to the most recent release
 2020-02-13 19:28:33 -06:00
Matthias Diener
03ce5effa1
charmpp: add version 6.10.0, switch to https for download (#14930) 2020-02-13 19:26:26 -06:00
Matthias Diener
eb88dfee9a
byobu: add version 5.131 (#14932) 2020-02-13 19:23:25 -06:00
eugeneswalker
1d25564230
libcircle depends on pkg-config for build (#14933) 2020-02-13 19:22:54 -06:00
Massimiliano Culpo
681ad2ac44
hepmc: fixed wrong sha256 for latest versions (#14926) 2020-02-13 07:49:21 -06:00
Matthias Wolf
268f42bf7e
py-binaryornot: new package (#14906) 2020-02-13 11:42:29 +01:00
Matthias Wolf
856734b804
py-poyo: new package (#14909) 2020-02-13 10:07:29 +01:00
Matthias Wolf
7252066a32
py-jinja2-time: new package (#14910) 2020-02-13 10:07:07 +01:00
Matthias Wolf
06c85ea5bf
py-elasticsearch: added v7.5.1 and v6.4.0 (#14913) 2020-02-13 10:06:01 +01:00
Matthias Wolf
3dd844e597
py-clustershell: new package (#14914) 2020-02-13 10:03:45 +01:00
Matthias Wolf
fb482ae0c9
py-magic: new package (#14912) 2020-02-13 10:03:18 +01:00
Matthias Diener
a337d27874
gdb: added v9.1 (#14919) 2020-02-13 09:51:04 +01:00
Federico Ficarelli
de84bd3f24
hipsycl: new package and new 'sycl' virtual package (#14051) 2020-02-13 07:32:39 +01:00
eugeneswalker
5243d270d4 bmi depends on automake for build 2020-02-12 21:58:35 -08:00
noguchi-k
38303a6a79
macsio: cast JsonGetInt from int to unsigned int (#14736) 
* macsio: cast from int to unsigned int

* macsio: apply a patch only when version is 1.1
 2020-02-12 20:13:26 -06:00
Chuck Atkins
90f3635afd
protobuf: Fix intel compiler failures. (#14916) 2020-02-12 16:21:43 -05:00
Jon Rood
7e50cec5a4
Adding Intel LLVM compiler (#13618) 
* Adding Intel LLVM compiler.

* Fixing some minor issues.

* Split build environment on run environment in intel-llvm.
 2020-02-12 12:30:04 -06:00
Dan Lipsa
ca66ab6901
Paraview: fix PYTHONPATH for static build. (#14648) 
* Fix PYTHONPATH for static build.

* Only for the latest version.
 2020-02-12 13:24:09 -05:00
Axel Huebl
3b2c534e73
openPMD-api: Build Env Fix & Dev (#14904) 
- fix a missing `env.` prefix in the build environment.
- rename development branch to same name as in git
 2020-02-12 10:02:01 +01:00
Axel Huebl
b5a3ee636b
WarpX: master is the new develop (#14898) 
WarpX removed the `dev` branch in favor of a simpler,
`master`-centric development model.
`master` is the new development branch and there is no
stable branch anymore (we use tags and release branches
instead).
 2020-02-11 20:47:50 -08:00
victorusu
78ce1c7ce4
New package: ReFrame (#14737) 2020-02-11 17:51:26 -08:00
Hadrien G
c8cb480eb7
ROOT: Add Pythia8 support (#14790) 2020-02-11 17:38:22 -08:00
darmac
cf120d7441
OpenCV package: add versions 4.2.0, 4.1.2, and 4.1.1(#14814) 2020-02-11 17:34:44 -08:00
Hadrien G
947dabc356
[dd4hep] Make DDDigi work with current TBB releases (#14791) 
Add patch for DDDigi's broken TBB support. The issue is fixed in
DD4hep master so the patch is only required for 1.11.0
 2020-02-11 17:17:05 -08:00
Sajid Ali
2c63ea49d1
New package: libvips (#14794) 2020-02-11 17:02:39 -08:00
darmac
630611a786
libdrm: add version 2.4.100 (#14809) 2020-02-11 16:57:18 -08:00
codeandkey
78f16d703d r-truncdist: new package at 1.0-2 2020-02-11 16:52:51 -08:00
Jen Herting
582e7ce2c8 [mono] add version 6.8.0.105 2020-02-11 16:49:35 -08:00
Scott Wittenburg
c2885990b8
Fix intel-mkl package (#14856) 
* Add cpio package

* intel-mkl: Depend on cli tool needed during build
 2020-02-11 16:21:49 -06:00
Seth R. Johnson
5c33f638d7
Fix QT4 platform detection for linux clang (#14891) 
* Fix QT4 platform name for linux clang

* Fix clang compiler flags on QT4
 2020-02-11 14:00:02 -06:00
Frédéric Simonis
e8b6c40b31
precice: add version 2.0.0 (#14842) 
Added python3 dependency
Added support for new CMake variables
 2020-02-11 10:06:03 +01:00
Matthias Diener
7706b76d3a
unifdef: added new package (#14880) 2020-02-11 10:03:44 +01:00
Christoph Junghans
1a41ec766a
heffte: added v0.2 (#14881) 2020-02-11 10:02:17 +01:00
darmac
35df75ee77
hepmc: added versions up to v3.2.0 (#14805) 2020-02-11 09:46:59 +01:00
Brian Van Essen
490508d324
Hydrogen: update dependency on aluminum (#14760) 
* Hydrogen now depends on `aluminum +nccl` vs. `aluminum +mpi_cuda`
* Hydrogen: Simplify Mac OS OpenMP-detection logic
* Aluminum: Add Mac OS OpenMP-detection logic
* LBANN: depend on conduit@0.4.0: instead of conduit@master
 2020-02-10 12:13:47 -08:00
Massimiliano Culpo
357786ce6b
Spack find: fix queries that specify dependencies (#14757) 
Fixes #10019

If multiple instances of a package were installed in a single
instance of Spack, and they differed in terms of dependencies, then
"spack find" would not distinguish specs based on their dependencies.
For example if two instances of X were installed, one with Y and one
with Z, then "spack find X ^Y" would display both instances of X.
 2020-02-10 11:22:21 -08:00
Peter Scheibel
4e32505770
libedit package: add version 3.1-20191231 (#14851) 
This new version of libedit can make use of an ncurses dependency
built with +termlib (which moves some symbols into a separate
libtinfo).
 2020-02-10 10:44:52 -08:00
Glenn P Johnson
37a6b8d54f Fix vim build with ^ncurses+termlib 
This PR will set the approriate library if ncurses is built with a
separate tinfo library.
 2020-02-10 10:25:35 -08:00
darmac
c77eeca61e icedtea: added versions up to v3.9.0 (#14806) 2020-02-10 11:08:45 +01:00
Glenn Johnson
745a843911 New package: r-biomartr (#14812) 
This PR creates the r-biomartr package as well as needed new packages
and updates.

- new dependency: r-philentropy
- update: r-curl
 2020-02-10 11:08:04 +01:00
Hadrien G
cb3dbea198 acts-core: added v0.16.0 (#14839) 
* Adapt to ACTS v0.16

* ACTS uses the DD4hep XML components nowadays
 2020-02-10 11:06:56 +01:00
Glenn Johnson
8aa1eba2e0 New package: r-watermelon (#14864) 
This PR creates the r-watermelon package, along with dependencies.

- new package: r-fdb-infiniummethylation-hg19
- new package: r-illuminahumanmethylation450kanno-ilmn12-hg19
- new package: r-lumi
- new package: r-methylumi
- new package: r-roc
- new package: r-txdb-hsapiens-ucsc-hg19-knowngene
- updated package: r-matrixstats, new version needed as a dependency
 2020-02-10 10:49:34 +01:00
Glenn Johnson
1ed0efec7d New package: r-suppdists (#14865) 2020-02-10 10:44:17 +01:00
Glenn Johnson
bd442e884a New package: r-imager (#14866) 
This PR adds the r-imager package and dependencies.

- new package: r-bmp
- new package: r-readbitmap
 2020-02-10 10:44:00 +01:00
Glenn Johnson
ad914c28d7 New package: r-proj (#14872) 2020-02-10 10:43:27 +01:00
Glenn Johnson
d00a3eda6b New package: r-proj4 (#14871) 2020-02-10 10:42:32 +01:00
Glenn Johnson
22df37c328 New package: r-pscbs (#14867) 
This PR adds the r-pscbs package along with new dependencies and updates.

- new package: r-aroma-light
- new package: r-r-cache
- updated package: r-r-oo
 2020-02-10 10:41:56 +01:00
Glenn Johnson
716978e00c New package: r-copula (#14874) 
This PR adds the r-copula package and dependencies.

- new package: r-adgoftest
- new package: r-gsl
- new package: r-pspline
- new package: r-stabledist
 2020-02-10 10:40:47 +01:00
Glenn Johnson
42c829adb4 New package: r-gsalib (#14873) 2020-02-10 10:38:44 +01:00
Kai Torben Ohlhus
4d173579cb openblas: added v3.8.0 (#14875) 2020-02-10 10:35:29 +01:00
darmac
f274d89c33 xterm: added versions up to v353 (#14829) 2020-02-10 09:44:50 +01:00
darmac
85b6e3e6d4 openldap: added v2.4.49 (#14815) 2020-02-10 09:40:46 +01:00
darmac
1c5838be5c pngquant : add depency on libpng (#14836) 2020-02-10 09:39:45 +01:00
Kai Torben Ohlhus
3ba5df3763 octave: add 5.2.0 (#14868) 
Add version Octave 5.2.0 including sha256.
 2020-02-09 21:04:09 -06:00