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 )
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url.
2020-02-13 20:10:02 -06:00
Adam J. Stewart
e0dfc3ddbf
Fix shell detection: zsh5 -> zsh ( #14858 )
2020-02-13 20:07:09 -06:00
Glenn Johnson
8beb42e749
New package: r-codex ( #14869 )
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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 )
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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 )
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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 )
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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 )
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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 )
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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 )
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As discussed in:
https://spackpm.slack.com/archives/C5VL7V81G/p1581394270058800
2020-02-13 19:45:09 -06:00
asmaahassan90
413de215b2
Fix run environment ( #14908 )
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* 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 )
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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
2020-02-13 19:30:10 -06:00
Cameron Stanavige
4b7f057a4b
unifyfs: remove numa dependency ( #14925 )
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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
Patrick Gartung
4dc67b79aa
Replace direct call to patchelf with get_existing_elf_rpaths which handles exceptions. ( #14929 )
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* Replace direct call to patchelf with get_existing_elf_rpaths which handles exceptions.
* Remove unused patchelf definition.
* Convert to set.
2020-02-13 11:34:20 -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 )
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* 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
Todd Gamblin
a7b43f1015
spack python: add -m option to run modules as scripts
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It's often useful to run a module with `python -m`, e.g.:
python -m pyinstrument script.py
Running a python script this way was hard, though, as `spack python` did
not have a similar `-m` option. This PR adds a `-m` option to `spack
python` so that we can do things like this:
spack python -m pyinstrument ./test.py
This makes it easy to write a script that uses a small part of Spack and
then profile it. Previously thee easiest way to do this was to write a
custom Spack command, which is often overkill.
2020-02-12 16:45:41 -08:00
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 )
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* 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 )
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* 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 )
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- 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 )
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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 )
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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
Todd Gamblin
c56c4b334d
bugfix: spack -V should use working_dir() instead of git -C
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- `git -C` doesn't work on git before 1.8.5
- `working_dir` gets us the same effect
2020-02-11 16:52:06 -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 )
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* 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 )
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* 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 )
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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
