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10286 Commits

Author SHA1 Message Date
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