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Author SHA1 Message Date
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