Michael Kuron
ff4a4fcd9e
siesta: add netcdf support ( #6431 )
2017-11-23 13:39:32 -07:00
George Hartzell
2a2670175d
boost@1.54 alse needs the call_once patch ( #6434 )
2017-11-23 20:17:17 +01:00
Michael Kuhn
5bbbfe9446
Introduce virtual dependency pkgconfig ( #5198 )
...
There are two providers, pkgconf and pkg-config, with the former being
the default provider.
2017-11-23 08:05:38 -07:00
Sergey Kosukhin
7f0659f032
New version and patch for 'sqlite'. ( #6303 )
2017-11-23 08:04:41 -07:00
Audrey Thoma
cd7d812be9
express: new package ( #6281 )
2017-11-23 08:04:02 -07:00
Ondřej Čertík
7a2b3b2588
Add a patch for Intel 18.0.1 ( #6392 )
2017-11-23 07:28:35 -07:00
Michael F. Herbst
a955f63530
Add bohrium to spack ( #6395 )
...
* Add bohrium package.py
* Changes suggested by @davydden
* Add +cuda guard
* Specify required environment setup
2017-11-23 07:24:55 -07:00
Eric
1dba6435bd
r-plotly: Create new package ( #6423 )
2017-11-23 07:17:17 -07:00
Denis Davydov
ddf10fa322
dealii: limit CMake to 3.9 as 3.10.0 is not supported yet ( #6427 )
2017-11-23 07:16:44 -07:00
sknigh
e2cf933ec1
gcc environment module will set CC, CXX, FC, F77, and F90 flags ( #3954 )
2017-11-23 12:44:55 +01:00
Cameron Smith
951679376e
zoltan: add optional dependency on parmetis ( #6387 )
2017-11-23 09:03:02 +01:00
Eric
6fd1009081
r-mixtools: Create new package ( #6421 )
2017-11-23 09:01:10 +01:00
Eric
bdd8bb1fd9
r-ranger: Create new package ( #6422 )
2017-11-23 09:00:32 +01:00
Chien-Chang Feng
630d7e19db
py-yt: Yt-project is moved. Add new version. ( #6409 )
2017-11-23 07:25:35 +01:00
Jon Rood
8b63cc6ad6
Using MPI environment compiler variables for pnetcdf. ( #6424 )
2017-11-22 21:34:21 -08:00
Massimiliano Culpo
0fc6611dc2
Changed every docs variant into doc as decided in #2663 ( #6412 )
...
fixes #2663
2017-11-22 15:06:59 +01:00
Sergey Kosukhin
d4ab511f73
Script for 'eccodes' is compatible with Python 3. ( #6402 )
2017-11-21 15:59:04 -07:00
Audrey Thoma
a0df5ae3e0
phantompeakqualtools: new package ( #6403 )
2017-11-21 15:58:20 -07:00
Eric
9e013ee036
r-pbapply: Create new package ( #6377 )
2017-11-21 13:45:12 -07:00
Eric
5a72d30816
r-ggjoy: Create new package ( #6399 )
2017-11-21 13:44:25 -07:00
Eric
60b50a7bd2
r-ica: Create new package ( #6400 )
2017-11-21 13:43:02 -07:00
Eric
d6a5310df5
r-cppprogress: Create new package ( #6398 )
2017-11-21 13:42:44 -07:00
Eric
d725904803
r-sdmtools: Create new package ( #6397 )
2017-11-21 13:42:28 -07:00
BenBrands
27b9d2614c
CMake: add 3.10.0 ( #6393 )
2017-11-21 08:04:53 -07:00
David Poliakoff
003f83db50
gotcha: new package ( #6391 )
...
* Initial stab at a package for Gotcha
* Commit with no boilerplate
* Flake8
2017-11-21 08:04:43 -07:00
Audrey Thoma
c4613b8e1f
mira: new package ( #6385 )
2017-11-21 08:04:08 -07:00
Michael F. Herbst
f0c0243cd4
Fix to allow installing pocl 0.14 again ( #6372 )
...
* Resolve issue 4669
* Use prefix path magic attribute
2017-11-21 08:03:36 -07:00
Yifan Zhu
5250c8eb0a
r-broom: new package ( #6282 )
2017-11-21 10:49:09 +01:00
Yifan Zhu
e3abc7bfa4
r-haven: created new package ( #6293 )
2017-11-21 09:54:43 +01:00
Yifan Zhu
b7189ecf9e
r-psych: created new package ( #6286 )
2017-11-21 09:40:10 +01:00
Yifan Zhu
ef8429c99c
r-modelr: created new package ( #6289 )
2017-11-21 09:26:44 +01:00
Eric
0743c5bde6
r-crosstalk: Create new package ( #6383 )
2017-11-20 21:52:58 -07:00
Eric
cd5e6a14bb
r-fnn: Create new package ( #6384 )
2017-11-20 21:52:39 -07:00
Audrey Thoma
8b2abfb28b
masurca: new package ( #6386 )
2017-11-20 21:51:35 -07:00
Eric
70ce7e2099
meme: add version 4.12.0 ( #6388 )
2017-11-20 21:50:46 -07:00
Eric
035cce2b81
py-biopython: add version 1.70 ( #6389 )
2017-11-20 21:50:25 -07:00
Eric
17e0b81463
r-ggridges: Create new package ( #6376 )
2017-11-20 14:18:16 -07:00
Eric
30b794254f
py-pysam: add version 0.13 ( #6382 )
2017-11-20 14:08:25 -07:00
BenBrands
93d5a91a56
dealii: fix HDF5 dependency ( #6374 )
2017-11-20 11:57:53 -07:00
BenBrands
83db25967e
Atlas: add 3.11.39 ( #6375 )
2017-11-20 11:57:34 -07:00
Eric
9040f34aba
r-tclust: Create new package ( #6380 )
2017-11-20 11:57:04 -07:00
Eric
1d69dbe7ae
r-diffusionmap: Create new package ( #6378 )
2017-11-20 11:56:47 -07:00
Eric
012acdc7a2
r-chemometrics: Create new package ( #6379 )
2017-11-20 11:56:33 -07:00
Denis Davydov
4e878c21cd
elpa: add 2017.05.002 and 2017.05.003 ( #5306 )
...
* elpa: add 2017.05.002 and 2017.05.03
* add a variant for optimization flags
2017-11-20 11:17:22 -07:00
Denis Davydov
34da07db9b
dealii: add cuda_arch variant via CudaPackage ( #6070 )
2017-11-19 12:39:13 -07:00
Adam J. Stewart
acbdf516f7
Add a new package for rlwrap ( #6371 )
2017-11-19 06:45:25 -07:00
lingnanyuan
cf3df2a321
r-dose: Create new package. ( #6355 )
2017-11-18 12:54:14 -07:00
Eric
20092adb94
r-vgam: Create new package ( #6363 )
2017-11-18 06:39:55 -07:00
Eric
618f4dff6d
r-bindrcpp: Create new package ( #6366 )
2017-11-18 06:36:39 -07:00
Eric
1c55a401b1
r-dtw: Create new package ( #6365 )
2017-11-18 06:35:47 -07:00
Eric
ebfc7bd7aa
r-som: Create new package ( #6364 )
2017-11-18 06:35:21 -07:00
Michael Kuron
e2fea1e1e6
siesta: new package ( #6346 )
...
* siesta: new package
* siesta: use libs instead of ld_flags everywhere
2017-11-17 19:01:15 -07:00
Stephen Hudson
b2f0306c6f
Mpi4py update ( #6342 )
2017-11-17 19:00:36 -07:00
Javier Cervantes
21da747a5d
hepmc: fix hash and urls, add new version 3.0.0 ( #6348 )
2017-11-17 18:59:52 -07:00
健美猫
8bc024d2d9
Add cluster.2017.5 and cluster.2018.1. ( #6349 )
2017-11-17 18:59:18 -07:00
lingnanyuan
9647038f27
r-rvcheck: Create new package. ( #6351 )
2017-11-17 18:59:00 -07:00
lingnanyuan
eda91bebd7
r-gosemsim: Create new package. ( #6352 )
2017-11-17 18:58:43 -07:00
lingnanyuan
d836d7e7ea
r-do-db: Create new package. ( #6353 )
2017-11-17 18:58:23 -07:00
lingnanyuan
c604638681
r-fgsea: Create new package. ( #6354 )
2017-11-17 18:58:01 -07:00
lingnanyuan
5c06255b24
r-clusterprofiler: Create new package. ( #6356 )
2017-11-17 18:57:40 -07:00
sknigh
1f8f593dd6
Added libhio 1.4.0.0 ( #6357 )
2017-11-17 18:57:17 -07:00
Brian Homerding
17debcb9b2
NuT: Add Installation of lib and demo app ( #6341 )
2017-11-16 16:30:42 -07:00
Matthias Vogelgesang
a62f8698c3
Add UFO and dependencies ( #6337 )
...
* Add json-glib
* Add ufo-core
* Add ufo-filters
2017-11-16 09:37:17 -08:00
healther
ef3c909701
add package py-numba ( #6323 )
...
* add package py-numba
* Update package.py
* Update package.py
* Update package.py
2017-11-16 10:13:20 -07:00
Audrey Thoma
e941f33eaf
meraculous: new package ( #6292 )
...
* meraculous: new package
* adding gcc version conflict
* Update package.py
* Update package.py
2017-11-16 09:40:46 -07:00
lingnanyuan
bb3d5fd313
r-rhdf5: Create new package. ( #6330 )
2017-11-16 09:40:15 -07:00
lingnanyuan
e732a554ff
r-shortread: Create new package. ( #6332 )
2017-11-16 09:30:18 -07:00
lingnanyuan
cca06422fa
r-sva: Create new package. ( #6333 )
2017-11-16 09:28:59 -07:00
David Hows
d89b09493c
Minor package fixes ( #6334 )
...
* Add no-implicit-fallthrough to MsgpackC
* Add 0.2.1 of Neovim
* Lint
2017-11-16 09:28:40 -07:00
Stephen Hudson
9d1224e5d8
py-petsc4py: Update version to 3.8.0 and add dependencies ( #5792 )
...
* py-petsc4py: Update version to 3.8.0 and add dependencies
- Added explicit dependency on python and numpy
* Kept old version - and corrected minimal python version
* Update to 3.8.1
2017-11-15 16:49:36 -07:00
baip
697f3ea71d
cp2k: add dependency on smm and libxc & new version 5.1 ( #6194 )
...
* cp2k: add libxsmm dependency
* cp2k: add libxc dependency
* cp2k: add smm variant to select from libxsmm or libsmm
* cp2k: add version 5.1
2017-11-15 16:49:08 -07:00
Christoph Junghans
7da8a02cbf
git grep --files-with-matches github.com/llnl/spack | xargs sed -i '/github.com/s@llnl/spack@spack/spack@' ( #6329 )
2017-11-15 16:46:39 -07:00
Denis Davydov
cb5fd6035a
intel: add 2018.1 ( #6322 )
2017-11-15 13:13:15 -07:00
Axel Huebl
d1a733bc86
xtensor, xtl, xsimd ( #6315 )
...
Adds the QuantStack libs (C++, header-only) needed for
xtensor.
2017-11-15 13:12:31 -07:00
Yifan Zhu
cde0570c56
r-janitor: created new package ( #6313 )
2017-11-15 13:09:24 -07:00
Yifan Zhu
0d9ab84ebb
r-dbplyr: created new package ( #6311 )
2017-11-15 13:09:11 -07:00
Howard Pritchard
af1b93b3db
Open MPI: add 2.0.4 release to package file ( #6310 )
...
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-11-15 13:03:07 -07:00
健美猫
71f12597a7
Update pgi to 17.10 . ( #6306 )
2017-11-15 13:02:54 -07:00
Sergey Kosukhin
e77b11674f
Update for 'magics' and 'libemos'. ( #6275 )
2017-11-15 13:01:23 -07:00
Benedikt Riedel
2eb7fabe62
Allow openblas to build on a VM ( #6258 )
...
This adds a "virtual_machine" boolean variant which adds build
options that enable building openblas on a VM.
2017-11-15 10:32:02 -08:00
Eric
9acf207023
picard: add versions and fix url format ( #6309 )
2017-11-14 16:41:27 -07:00
Michael Kuhn
ec5d366bcd
likwid: Fix hash for 4.3.0 ( #6307 )
...
Prefer 4.2.1 for now because 4.3.0's hash changes regularly.
2017-11-14 16:41:05 -07:00
健美猫
d9a4e7a038
Update miniconda to 4.3.30. ( #6233 )
2017-11-14 12:11:53 -08:00
Adam J. Stewart
138e9d08c6
Add the latest version of Lmod ( #6297 )
2017-11-14 10:32:41 -08:00
koebbe
50957bd44f
py-h5py: make sure to depend on the hl variant of hdf5 ( #6304 )
2017-11-14 09:26:58 -07:00
vishalkenchan
0692029273
update trilinos checksums ( #6301 )
2017-11-14 09:22:34 -07:00
Michael Kuhn
aa27432a1d
ncl: Check for ncl binary after installation ( #6298 )
...
ncl's build system will happily continue in case of errors, which might
result in the ncl binary not being built.
2017-11-14 09:22:04 -07:00
Michael Kuhn
e31b997162
icu4c: Update to 60.1 ( #6295 )
...
Previous versions try to include xlocale.h, which fails on glibc >= 2.26.
2017-11-14 09:21:35 -07:00
Yifan Zhu
a8f9182ef3
r-forcats: created new package ( #6291 )
2017-11-14 09:21:21 -07:00
Michael Kuhn
93bca2f3a2
libbson, libmongoc: Update to 1.8.1 ( #6290 )
2017-11-14 09:21:05 -07:00
Eric
137a9e64ac
trimgalore: add version 0.4.5 ( #6288 )
2017-11-14 09:20:20 -07:00
Yifan Zhu
392e25b7e6
r-mnormt: created new package ( #6287 )
2017-11-14 09:20:06 -07:00
Yifan Zhu
05eb287ed9
r-bindr: created new package ( #6285 )
2017-11-14 09:19:49 -07:00
Yifan Zhu
c042644b53
r-glue: created new package ( #6283 )
2017-11-13 16:25:52 -07:00
Douglas Duckworth
c7d2b4dbd6
relion 2.1 - update variant defaults ( #6201 )
...
Default precision should be double for CPU. Generally users also want
to use GPUs so the +cuda variant is now also enabled by default.
2017-11-13 12:29:43 -08:00
Christoph Junghans
bde727e187
mpibash: move to autotools ( #6253 )
2017-11-13 10:48:31 -07:00
Christoph Junghans
02335fa849
ucx: initial commit ( #6265 )
2017-11-13 10:47:58 -07:00
Eric
306aca812d
ont-albacore: add version 2.1.2 ( #6278 )
2017-11-13 10:47:40 -07:00
Satish Balay
6fd92e4257
petsc: update to version 3.8.2 ( #6244 )
...
Includes pkgconfig fix [for mfem static build failure]
2017-11-11 07:16:03 -07:00
Brian Homerding
19f8940c01
Nekbone: Installing data files for example runs ( #6243 )
...
* Nekbone: Installing data files for example runs
* Typo Fix
2017-11-10 19:59:33 -07:00
Sergey Kosukhin
263126bc5d
Create symlink for 'swig' binary after installation. ( #6240 )
2017-11-10 19:50:11 -07:00
Aaron Fisher
af06ea0e74
Fixed mfem mpi build issue. ( #6254 )
...
* Fixed mfem mpi build issue.
* Fixed a non-mpi build issue and switched to the latest official MFEM release.
2017-11-10 19:49:17 -07:00
Yifan Zhu
e38f31e773
feature/r-reprex: new package ( #6257 )
2017-11-10 19:47:21 -07:00
Cyrus Harrison
b079e1dbd5
add alpine ascent ( #6224 )
...
* add ascent package and and deps
* proper use of site_packages_dir prop
* flake8
* add maitain, small updates
* flake8
* flake8
* fixs for docstrings for sphinx
2017-11-10 17:00:47 -08:00
becker33
917d021997
Add version 1.04 ( #6259 )
2017-11-10 15:52:48 -08:00
becker33
a7b817b494
elfutils: add --no-as-needed flag for library ordering issue ( #6256 )
...
* add --no-as-needed flag for library ordering issue libelf
* fix syntax error.
2017-11-10 11:42:37 -08:00
Yifan Zhu
f6ed8d856a
xclip: created new package ( #6248 )
2017-11-10 11:13:00 -07:00
Yifan Zhu
a872dc5927
r-clipr: created new package ( #6249 )
2017-11-10 11:11:45 -07:00
lingnanyuan
acc3817ffc
r-purrr: Create new package. ( #6241 )
2017-11-09 14:51:30 -07:00
lingnanyuan
65a278c927
r-covr: Create new package. ( #6239 )
2017-11-09 13:19:53 -07:00
lingnanyuan
e43e29209d
r-readxl: Create new package. ( #6238 )
2017-11-09 13:19:43 -07:00
lingnanyuan
0902f58f3d
r-cellranger: Create new package. ( #6237 )
2017-11-09 13:19:25 -07:00
lingnanyuan
5e0e3092f6
r-rematch: Create new package. ( #6236 )
2017-11-09 13:19:12 -07:00
Satish Balay
2b07379831
petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configur… ( #6189 )
...
* petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configured with zlib
* petsc: fix dependency [of zlib to be on hdf5 - and not on petsc]
* petsc: use the fact that hdf5/package.py has a hard dependency on zlib [so no need to check for this dependency in code]
recommended-by: @davydden
* petsc: change hdf5 dependency to 'hdf5+hl' as petsc configure is looing for -lhdf5_hl
https://github.com/spack/spack/issues/5846
2017-11-09 11:34:59 -08:00
Satish Balay
8d512ce9ae
magma: cuda updates [from xsdk-0.3.0 branch] ( #6160 )
...
- add gcc dependency per cuda versions
- Fix for cuda-9.0 as it does not support sm20
nvcc fatal : Unsupported gpu architecture 'compute_20'
2017-11-09 11:34:40 -08:00
lingnanyuan
ee867db5de
r-log4r: Create new package. ( #6133 )
2017-11-09 10:23:48 -07:00
Simone Bnà
c79a0fbbf2
mesa: fixed url for version ( #5818 )
2017-11-09 10:16:52 -07:00
Benedikt Riedel
266de67c24
ROOT needs to have a consistent version of binutils, as it is very sensitive to the version of libopcodes. You can't move the code from one system (with the same OS) as another. ( #6226 )
2017-11-09 06:49:27 -08:00
lingnanyuan
935a6b00d7
r-analysispageserver: Create new package. ( #6135 )
2017-11-09 07:23:10 -07:00
Levi Baber
74d38b3150
py-dlcpar ( #6229 )
...
* py-dlcpar: new package
* py-dlcpar: whitespace
2017-11-09 07:21:56 -07:00
baip
acf6653933
pexsi: add version 0.10.2 ( #6232 )
2017-11-09 07:21:39 -07:00
David Gardner
d9fc26b2a5
add sundials 3.1.0 ( #6230 )
2017-11-09 14:04:03 +01:00
Luigi Calori
24bb3c61de
fix perl dependent modules, #5900 ( #5937 )
...
* FIX perl dependent environmwent setup to avoid void lines in generated modules as #5900
* remove debug prints
* fix flake8
2017-11-08 22:10:50 -07:00
Alfredo Adolfo Gimenez
a754bd7eee
Package/sosflow ( #6122 )
...
* Added missing deps to libffs
* SOSflow spack package pointing to sos_flow feature/spack branch
* Using tag for spack build
* Change url to spack/spack
2017-11-08 22:07:37 -07:00
David Gardner
a656bc300a
add patch for building sundials ( #6161 )
...
* add patch for building sundials on mac
* add upper limit on the patch
2017-11-08 22:06:34 -07:00
Yifan Zhu
3159841e33
r-callr: created new package ( #6223 )
2017-11-08 21:59:21 -07:00
lingnanyuan
72bec9a7a0
r-rex: Create new package. ( #6221 )
2017-11-08 21:57:09 -07:00
Yifan Zhu
ca2ffd9299
r-rvest: created new package ( #6220 )
2017-11-08 21:56:50 -07:00
Levi Baber
ef126523f1
fastme: new package ( #6219 )
2017-11-08 21:56:32 -07:00
Yifan Zhu
edc1e6a0d8
r-selectr: created new package ( #6218 )
2017-11-08 21:56:02 -07:00
lingnanyuan
e57564e899
r-tseries: Create new package. ( #6216 )
2017-11-08 21:55:45 -07:00
sknigh
699748a2be
Added missing build dependency to json-c ( #6211 )
2017-11-08 21:55:28 -07:00
lingnanyuan
e2004076b1
r-allelicimbalance: Create new package. ( #6044 )
2017-11-08 21:52:46 -07:00
Yifan Zhu
ac7f5a1af1
r-mzr: created new package ( #6206 )
2017-11-08 19:53:00 -07:00
Yifan Zhu
cd4b19ffa8
r-msnbase: new package ( #6207 )
2017-11-08 19:52:38 -07:00
lingnanyuan
912d39908d
r-sqldf: Create new package. ( #6208 )
2017-11-08 19:52:08 -07:00
lingnanyuan
4585d6426a
r-gsubfn: Create new package. ( #6209 )
2017-11-08 19:51:51 -07:00
Yifan Zhu
b110cd0b12
r-vsn: new package ( #6210 )
...
* r-hexbin: updated md5
* r-vsn: created new package
2017-11-08 19:51:35 -07:00
lingnanyuan
7848e0d4b6
r-quantmod: Update version to 0.4-11 ( #6212 )
2017-11-08 19:51:13 -07:00
Yifan Zhu
ecdaea1c8e
r-xml2: created new package ( #6217 )
2017-11-08 19:50:53 -07:00
lingnanyuan
1c2292dcd4
r-timedate: Create new package. ( #6215 )
2017-11-08 19:50:37 -07:00
lingnanyuan
5558cce438
r-fracdiff: Create new package. ( #6214 )
2017-11-08 19:50:18 -07:00
lingnanyuan
2cd57876c7
r-forecast: Create new package. ( #6213 )
2017-11-08 19:49:58 -07:00
Christoph Junghans
b3f678c1c0
gasnet: add 1.30.0 ( #6167 )
...
* gasnet: add 1.30.0
* gasnet: expose more options as variants
* gasnet: change defaults
2017-11-08 19:43:13 -07:00
Audrey Thoma
877bee3cb5
guidance: new package ( #6079 )
...
* guidance: new package
* not really fixed yet
* adding loop
* fixing url
* dang typos
2017-11-08 14:07:13 -07:00
lingnanyuan
dd3a6d7f18
r-ampliqueso: Create new package. ( #6132 )
2017-11-08 14:05:53 -07:00
Yifan Zhu
96f70606e8
r-tiff: created new package ( #6134 )
2017-11-08 14:05:33 -07:00
lingnanyuan
f73b409968
r-anaquin: Create new package. ( #6138 )
2017-11-08 14:05:17 -07:00
lingnanyuan
2cba0d4d5f
r-qvalue: Create new package. ( #6137 )
2017-11-08 14:05:00 -07:00
baip
4273ebac3c
libxsmm: add libs property ( #6193 )
2017-11-08 14:04:26 -07:00
lingnanyuan
17b9a479b6
r-aneufinderdata: Create new package. ( #6192 )
2017-11-08 14:03:35 -07:00
lingnanyuan
bb619aa091
r-aneufinder: Create new package. ( #6191 )
2017-11-08 14:03:22 -07:00
Christoph Junghans
d8db861fec
flecsi: fix build ( #6168 )
2017-11-08 14:03:05 -07:00
lingnanyuan
04f32377b2
r-rhtslib: Create new package. ( #6164 )
2017-11-08 14:02:12 -07:00
Audrey Thoma
3fcc911737
kraken: new package ( #6163 )
2017-11-08 14:01:55 -07:00
Audrey Thoma
743a87abb3
fpc: new package ( #6162 )
2017-11-08 14:01:31 -07:00
lingnanyuan
6556a5c914
r-cowplot: Create new package. ( #6190 )
2017-11-08 13:58:57 -07:00
Yifan Zhu
5f70d578ec
r-maldiquant: created new package ( #6188 )
2017-11-08 13:58:43 -07:00
lingnanyuan
860834e094
r-reordercluster: Create new package. ( #6187 )
2017-11-08 13:58:21 -07:00
Yifan Zhu
605c8e65b3
r-mzid: created new package ( #6186 )
2017-11-08 13:58:04 -07:00
Yifan Zhu
98baf49ba6
r-xde: created new package ( #6185 )
2017-11-08 13:57:46 -07:00
lingnanyuan
3943bc945b
r-ggdendro: Create new package. ( #6184 )
2017-11-08 13:57:30 -07:00
lingnanyuan
241e1b56b5
r-dnacopy: Create new package. ( #6183 )
2017-11-08 13:57:15 -07:00
Yifan Zhu
92a582d5f8
r-mergemaid: created new package ( #6182 )
2017-11-08 13:56:59 -07:00
lingnanyuan
146db9adef
r-bamsignals: Create new package. ( #6181 )
2017-11-08 13:56:34 -07:00
Yifan Zhu
87aafeb78a
r-xmapbridge: created new package ( #6180 )
2017-11-08 13:56:15 -07:00
Sergey Kosukhin
c7a855ba57
Missing dependency for 'cdo'. ( #6175 )
2017-11-08 13:55:57 -07:00
baip
ed00757265
gcc: add 5.5.0 ( #6171 )
2017-11-08 20:27:08 +01:00
vishalkenchan
392929ba77
lammps: add more packages ( #6174 )
...
* lammps : adding new varients and dependencies therein
* Update package.py
* removing trailing whitespaces
2017-11-08 09:01:14 -07:00
Matthew Scott Krafczyk
00d48e60bf
Fix for nghttp2 installation ( #5904 )
...
nghttp2 depends on python, and requires the install directory to exist,
and contain the python module directory which it will eventually
install the python modules into.
2017-11-07 15:59:15 -08:00
James Dickson
841d42b308
TyphonIO: new package + Updated MACSio package ( #6177 )
2017-11-07 13:13:06 -07:00
Audrey Thoma
8bae192d5c
repeatmasker: new package ( #6108 )
2017-11-06 17:27:42 -07:00
Michael Kuhn
ca73103dac
Introduce static_to_shared_library function ( #6092 )
...
The static_to_shared_library function takes an existing static library
and produces a shared library based on it.
2017-11-06 17:21:46 -07:00
Satish Balay
dc78e60c83
trilinos: update hdf5 dependency to use 'hdf5+hl' ( #6025 )
...
* trilinos: update hdf5 dependency to use 'hdf5+hl'
Without this change - I get the following error [triggered by 161dca6d5c9810f808
2017-11-06 13:03:06 -08:00
Luigi Calori
f0d33df3a9
some missing X11 "*proto" dependencies ( #6158 )
...
* fix xinput deps
* adding other x11 proto missing deps, see #6157
2017-11-06 13:02:05 -08:00
Satish Balay
436ebc4490
petsc: update petsc dependency on superlu-dist ( #6159 )
2017-11-06 12:52:10 -08:00
Yifan Zhu
cd4d26705e
Bioconductor package url change ( #5797 )
2017-11-06 11:17:59 -07:00
Michael Kuhn
450f2fa034
likwid: Use external lua if possible ( #6009 )
2017-11-06 11:14:34 -07:00
Douglas Duckworth
47b15feec3
added new package - MotionCor2 ( #6151 )
2017-11-06 11:09:46 -07:00
Denis Davydov
f538b7ac3e
dealii: make sure bundled libs are not used ( #6106 )
2017-11-06 12:38:59 +01:00
Besnard Jean-Baptiste
84c6fea32e
Graphviz : Add a GTS variant ( #6149 )
...
Enable support for the GNU Triangulated Surface Library
- New variant +gts for graphviz
- Optionnal dependency for GTS (already packaged)
2017-11-05 16:55:44 -08:00
Douglas Duckworth
ccc51cea7d
added relion v 2.1 ( #6023 )
...
* added relion v 2.1
* relion 2.1 - misssed comma
* relion now pulling from master branch - removed 2.03 - added cuda 8 as dependency given 9 does not yet work with relion per https://github.com/3dem/relion/issues/296
2017-11-05 15:01:21 -08:00
Ben Boeckel
22df09315f
Re-add list_url for all R packages ( #6110 )
...
* r-igraph: find old packages in the archive
Fixes #6104 .
* r-irlba: find old packages in the archive
Fixes #6101 .
* r-lazyeval: find old packages in the archive
Fixes #6102 .
* packages: set list_url for all packages hosted on CRAN
* packages: consistently use the CRAN archive URLs
2017-11-05 13:42:24 -08:00
Adam Moody
2a8c97d440
dtcmp: add v1.1.0 ( #6146 )
2017-11-05 09:25:03 -08:00
Satish Balay
d34d0d6cbc
petsc: update to version 3.8.1 ( #6150 )
...
* petsc: update to version 3.8.1
* petsc: add in conflict between petsc-3.8.0 & mkl
2017-11-05 09:24:42 -08:00
Axel Huebl
5d9dd24daa
ISAAC 1.3.3 ( #6152 )
...
Add a new release of ISAAC.
2017-11-05 09:24:18 -08:00
Todd Gamblin
05fa302655
Replace github.com/llnl/spack with github.com/spack/spack ( #6142 )
...
We moved to a new GitHub org! Now make the code and docs reflect that.
2017-11-04 17:08:04 -07:00
vishalkenchan
386e0af089
add rol variant ( #6105 )
2017-11-04 12:14:46 -07:00
Yifan Zhu
9d234c4f8e
r-yapsa: created new package ( #6121 )
2017-11-03 14:21:00 -06:00
Yifan Zhu
fb1160d052
r-keggrest: created new package ( #6120 )
2017-11-03 14:20:36 -06:00
lingnanyuan
3921948b03
r-statmod: Create new package. ( #6119 )
2017-11-03 14:20:14 -06:00
lingnanyuan
b204c7e793
r-deseq: Create new package. ( #6118 )
2017-11-03 14:19:38 -06:00
lingnanyuan
f91c25ddee
r-samr: Create new package. ( #6117 )
2017-11-03 14:19:16 -06:00
lingnanyuan
d54627659a
r-impute: Create new package. ( #6116 )
2017-11-03 14:18:46 -06:00
lingnanyuan
95e290eaf3
r-altcdfenvs: Create new package. ( #6115 )
2017-11-03 14:18:17 -06:00
lingnanyuan
64689bdb01
r-makecdfenv: Create new package. ( #6114 )
2017-11-03 14:17:58 -06:00
lingnanyuan
b614c7970b
r-hypergraph: Create new package. ( #6113 )
2017-11-03 14:17:36 -06:00
Axel Huebl
5a4544ab05
ISAAC 1.3.2 ( #6129 )
...
Add a new release of ISAAC.
2017-11-03 14:58:38 +01:00
Ben Boeckel
be01b2d5f0
aspell: refuse to work with non-global extensions
...
Aspell compiles in the paths it looks for rather than looking relative
to its binary location. There are also no environment variables to
redirect it other than changing the path to the configuration file it
looks at.
2017-11-02 18:45:40 -07:00
Ben Boeckel
a81485cb3f
perl: support extensions in views
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
643a28aac5
python: extensions support for easy-install.pth
2017-11-02 18:45:40 -07:00
Ben Boeckel
d5a3d9d20e
view: test conflicting packages in views
2017-11-02 18:45:40 -07:00
Ben Boeckel
13b669de8e
view: test that extension paths exist
2017-11-02 18:45:40 -07:00
Ben Boeckel
41dfba0ba1
extension1: add a second version
2017-11-02 18:45:40 -07:00
Ben Boeckel
a7925bb927
bdftopcf: require xproto and fontsproto at build time ( #6112 )
...
These are technically "link" depends of libxfont, but they have no
actual libraries.
Fixes #5936 .
2017-11-02 15:47:18 -06:00
lingnanyuan
13f1781bea
Add package r-reportingtools and update url for its dependencies. ( #6071 )
...
* r-reportingtools: Create new package.
* r-go-db: Update url.
* r-gseabase: Update url.
* r-pfam-db: Update url.
2017-11-02 14:21:32 -06:00
Michael Kuhn
d1db161aeb
adios: Fix hdf5 and sz dependencies ( #6016 )
...
- hdf5's +hl variant is required because the build uses libhdf5_hl.
- sz is only compatible up to version 1.4.10 because the library has
been renamed to libSZ in 1.4.11.
2017-11-02 13:41:25 -06:00
Brice Goglin
3a1b013291
hwloc: add version 1.11.8 ( #6099 )
...
Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
2017-11-02 13:40:46 -06:00
Audrey Thoma
f9341857c7
arlecore: new package ( #6109 )
2017-11-02 13:40:03 -06:00
Christoph Junghans
c4db3d384e
gromacs: add develop version ( #6098 )
2017-11-02 15:16:21 +01:00
Adam J. Stewart
e47ceefc43
sundials+hypre depends on hypre ( #6075 )
2017-11-02 08:16:43 +01:00
Denis Davydov
11ba60413b
the-silver-searcher: add missing dependency ( #6095 )
2017-11-02 08:10:40 +01:00
Michael Kuhn
61ed583266
xqilla: Use append instead of extend ( #6094 )
2017-11-02 08:09:24 +01:00
Brian Van Essen
932068d725
Update candle ( #6097 )
2017-11-01 23:58:55 -06:00
Yifan Zhu
7d0c6361ee
r-getoptlong: created new package ( #6069 )
2017-11-01 19:09:54 -06:00
Yifan Zhu
f15969d624
r-gtrellis: created new package ( #6088 )
2017-11-01 19:09:20 -06:00
Brian Van Essen
86b7b84ddf
LBANN flags and OpenCV variant ( #5951 )
...
* Fixed the datatype flag in the LBANN package.
Fixed where the datatype flag should be set.
* Added variant to OpenCV to disable building DNN support
* Fixed a bug in how the elemental package tries to find its Fortran
library. The current method does not work with Intel compilers.
* Added necessary paths for cuDNN and CUB.
* Addressed flake8 issues in Elemental package.
* Fixed several flake8 errors. Added variant to build with or without
support for arbitrary-precision floating point arithmetic.
* Added the proper CMake flag when MPFR support is disabled.
* Fixed a bug in how the cudnn path was being set when there was no
cudnn requested. Also requested that OpenCV is built without eigen
support.
* Fixed another bug where a dependency may not be there and thus should
not be always checked.
2017-11-01 17:25:28 -07:00
Michael Kuhn
0d624eac55
lua: Build a shared library ( #6008 )
...
Patch is inspired by Arch Linux and Homebrew.
2017-11-01 17:10:14 -06:00
Yifan Zhu
f3af8272f5
r-circlize: new package ( #6087 )
2017-11-01 17:08:46 -06:00
lingnanyuan
ef240f59b8
r-alsace: Create new package. ( #6064 )
2017-11-01 17:04:56 -06:00
Yifan Zhu
26ade0c9ae
r-globaloptions: new package ( #6068 )
2017-11-01 17:04:38 -06:00
lingnanyuan
a05cca49d8
r-affycoretools: Create new package and its dependency r-ff. ( #6082 )
...
* r-ff: Create new package
* r-affycoretools: Create new package.
* r-ff: update url.
2017-11-01 17:04:17 -06:00
lingnanyuan
541818ed06
r-agimicrorna: Create new package. ( #6083 )
2017-11-01 17:03:48 -06:00
Yifan Zhu
616a43b76d
r-complexheatmap: created new package ( #6084 )
2017-11-01 17:03:30 -06:00
Yifan Zhu
ebff5086d7
r-shape: created new package ( #6086 )
2017-11-01 17:03:15 -06:00
Yifan Zhu
7fb6fbea54
r-pmcmr: new package ( #6085 )
2017-11-01 17:02:58 -06:00
Brian Van Essen
0c075b4923
Opencv eigen ( #6014 )
...
* Added a package for the MDAnalysis toolkit.
* Changed dependency for the eigen library to not include support for
multiple-precision (arbitrary-precision) floating point arithmetic,
since OpenCV does not support these data types.
* Fixed incorrect implementation
2017-11-01 13:50:06 -07:00
Mark Grondona
165e6bfe5f
flux: update flux-core to v0.8.0 ( #5914 )
...
* dockbook: remove update to dependent environment
Remove override of setup_dependent_environment in both docbook-xml
and docbook-xsl, which seems to generate a warning from spack about
"Suspicious requests to set or unset 'XML_CATLOG_FILES' found."
* flux: update version/dependencies to 0.8.0
Update flux-core to v0.8.0. Clean up dependencies and remove unneeded
extra invocation of ./autogen.sh when building from @master.
* flux: modify environment for Lua tests
Modify Spack environment to add `./?.lua` to LUA_PATH so that
fluxometer.lua can be found by tests during `make check` run
from `spack install --tests all flux`
* flux: fix broken flux version when on master
When building @master with spack, the flux version test from
`make check` fails because spack is using a shallow clone. Add
a setup section for @master that calls git pull --depth=50 --tags
to pull down tags and (hopefully) enough information for git-describe
to work properly.
2017-11-01 08:53:37 -07:00
Satish Balay
445ffc46a1
mfem does not use cmake for builds [anymore] - so remove code corresponding to this dependency. ( #6073 )
...
This enables mfem build on OSX [with xcode/clang compilers]
2017-11-01 08:52:03 -07:00
Elsa Gonsiorowski
b53adc90f7
MACSio and JSON-CWX packages ( #6018 )
2017-10-31 19:07:00 -06:00
Patrick Gartung
8a812294e0
Preinstall some llvm shared libraries so tblgen will work. ( #5988 )
2017-10-31 18:34:33 -06:00
Yifan Zhu
0ecef7d7f8
r-somaticsignatures: created new package ( #6065 )
2017-10-31 18:31:06 -06:00
lingnanyuan
1ec8f6ea3f
r-nloptr: Create new package. ( #6063 )
2017-10-31 18:30:49 -06:00
lingnanyuan
cfb685aa32
r-ptw: Create new package. ( #6062 )
2017-10-31 18:29:45 -06:00
lingnanyuan
aa1808c9a1
r-iso: Create new package. ( #6061 )
2017-10-31 16:17:53 -06:00
lingnanyuan
6af19477ef
r-nnls: Create new package. ( #6060 )
2017-10-31 16:17:36 -06:00
lingnanyuan
77b29288e6
r-als: Create new package. ( #6059 )
2017-10-31 16:17:21 -06:00
Yifan Zhu
10fcd9382a
r-ggbio: new package ( #6058 )
2017-10-31 16:17:07 -06:00
Bill Williams
f5e68879db
Fix spack build for RAJA: master requires submodules ( #6052 )
...
* Fix spack build for RAJA: master requires submodules
* Rename version: git to develop
2017-10-31 15:08:32 -06:00
Scott Wittenburg
3cb2d5341d
Fix incorrect checksum value for adios2 tarball ( #6054 )
2017-10-31 15:08:08 -06:00
lingnanyuan
6427406fc6
r-gviz: Create new package. ( #6043 )
2017-10-31 15:06:30 -06:00
Brian Homerding
8a86016bef
Added fftw dependency ( #6057 )
2017-10-31 14:33:01 -06:00
Brian Homerding
180dcfc652
sw4lite: Added -lgfortran and set to serial build ( #6055 )
...
* Added -lgfortran and set to serial build
* Update package.py
2017-10-31 14:29:06 -06:00
Christoph Junghans
d98e337706
ecp-proxy-suite: add nekbone and candle-benchmarks ( #6053 )
2017-10-31 13:11:08 -06:00
Christoph Junghans
182c11dd92
nekbone: add v17 ( #5978 )
2017-10-31 10:47:24 -06:00
Christoph Junghans
178107699c
candle-benchmarks: initial commit ( #6020 )
2017-10-31 09:11:04 -06:00
Christoph Junghans
ea35f49cdd
flang: fixed a typo ( #6048 )
2017-10-31 14:21:29 +01:00
Nils Deppe
4997291bf4
Add v3.2 of Blaze library ( #5992 )
2017-10-31 08:33:55 +01:00
George Hartzell
e69542c019
Fix tarball URL's for htslib ( #5993 )
...
A recent update (#5907 ) to htslib added a different URL for an old
version of htslib.
Now the package is using that URL as the pattern for the newer
versions too.
I have a vague memory of running into this before, that it's a known
issue.
This fixes it by adding an explicit `url_for_version` routine.
2017-10-30 22:49:52 -06:00
David Gardner
10b27ec788
sundials: update to v3.0.0 ( #6004 )
2017-10-30 22:49:13 -06:00
Jon Rood
50d932d9f1
Merging netcdf dependency lines in trilinos into one line for better coverage. ( #5990 )
2017-10-30 22:48:21 -06:00
Satish Balay
f5863d6708
superlu_dist: update to v5.2.2 ( #6024 )
2017-10-30 22:46:41 -06:00
Yifan Zhu
a31a1fef28
r-progress: new package ( #6034 )
...
* r-progress: created new package
* added version
2017-10-30 22:43:57 -06:00
Yifan Zhu
a97068a861
r-prettyunits: created new package ( #6033 )
2017-10-30 22:43:20 -06:00
lingnanyuan
6ddba08434
r-seqinr: Update version to 3.4-5 ( #6032 )
2017-10-30 22:42:51 -06:00
Yifan Zhu
8cc3bcb649
r-ggplot2: dependecy r-scales version should be 0.4.1: ( #6031 )
2017-10-30 22:42:31 -06:00
Yifan Zhu
fb072d1472
r-scales: added dependencies and version 0.5.0. ( #6030 )
...
* r-scales: Update url.
* r-scales: added version 0.5.0 and dependencies
2017-10-30 22:42:05 -06:00
lingnanyuan
7e4ac9a559
r-segmented: Update version to 0.5-2.2 ( #6029 )
2017-10-30 22:41:32 -06:00
Yifan Zhu
34c6ff10e9
r-ggally: new package ( #6036 )
...
* r-ggally: created new package
* r-ggally: version modified
2017-10-30 22:41:12 -06:00
lingnanyuan
65785cc3f5
r-speedglm: Create new package. ( #6035 )
2017-10-30 22:40:48 -06:00
lingnanyuan
a4138b6041
r-alpine: Create new package. ( #6037 )
2017-10-30 22:40:25 -06:00
Yifan Zhu
22f9125164
r-ensembldb: created new package ( #6038 )
2017-10-30 22:39:54 -06:00
Yifan Zhu
2a7027e2cc
r-pcamethods: created new package ( #6041 )
2017-10-30 22:39:29 -06:00
Yifan Zhu
cbb433655c
r-proxy: created new package ( #6039 )
2017-10-30 22:39:05 -06:00
lingnanyuan
8271434632
r-backports: Create new package. ( #6040 )
2017-10-30 22:38:35 -06:00
lingnanyuan
81d3c9fdc6
r-biovizbase: Create new package. ( #6042 )
2017-10-30 22:38:10 -06:00
Abhinav Bhatele
b37c8fef74
ecp-proxy-apps: release number changed to 1.0 ( #6049 )
2017-10-30 22:37:09 -06:00
Abhinav Bhatele
347c76b7a0
comd: update the git repo ( #6027 )
...
git repo has moved from exmatex to ECP-copa
2017-10-30 14:47:16 -06:00
George Hartzell
e6bc45a04a
Add bowtie2@2.3.0, fix dependencies and sbangs ( #5834 )
...
* Add bowtie2@2.3.0, fix dependencies and sbangs
Add support for bowtie2@2.3.0
- digest
- a patch for 2.3.0 that parallels the existing package. Truth be
told it builds (for me) without this, but I'm assuming that they're
there for a reason...).
- tune up dependencies
- need tbb
- don't need readline or zlib
Several things were installed with sbang's that use `/usr/bin/env` to
fine perl or python. Fix the dependency and clean up the sbang lines.
* Fix python exe name, avoid path banging
I'd cut and pasted the python bit from the perl bit and missed one
reference to perl.
While I'm there, use the cleaner `spec['perl'].command` instead of
banging together the path from its bits.
* Fix up the "when" constraints on the dependencies
Get the edge cases right.
- 2.2.5 doesn't need tbb, 2.3.[01] do.
- 2.3.1 needs readline and zlib.
2017-10-29 15:40:00 -06:00
Denis Davydov
957ded209a
add updated 2017 versions of Intel packages ( #5957 )
2017-10-29 15:38:10 -06:00
mmwolf
73fb02229a
Changed from setting C compiler to setting C++ compiler ( #6011 )
2017-10-29 07:42:27 -06:00
Denis Davydov
f6a8ae230e
dealii: remove bzip2 dependency for newer versions ( #6022 )
2017-10-29 07:39:51 -06:00
Yifan Zhu
56c7832789
r-iranges: changed url to git and added versioned dependency on r ( #5971 )
2017-10-28 12:14:33 -06:00
Audrey Thoma
f340333e6e
r-geomorph and other r fixes ( #5961 )
2017-10-28 12:13:38 -06:00
lingnanyuan
57611397c9
r-e1071: Add list_url. ( #5986 )
2017-10-28 12:12:52 -06:00
Michael Kuhn
b43e2d2546
likwid: Update checksum ( #6007 )
2017-10-28 12:12:21 -06:00
Yifan Zhu
43c1bb5f30
r-organismdbi: new package ( #5997 )
2017-10-28 12:11:44 -06:00
lingnanyuan
3eab6ed4b2
r-aldex2: Create new package. ( #6015 )
2017-10-28 12:10:22 -06:00
Christoph Junghans
167f7d0cdd
legion: add v17.10.0 ( #6019 )
2017-10-28 12:09:39 -06:00
Audrey Thoma
edae3ceae7
fixing abyss ( #5973 )
2017-10-28 17:05:52 +02:00
Sergey Kosukhin
5ebddcd5e3
Bugfix: from_list_url(). ( #5780 )
...
This fixes a bug in from_list_url where it was referring to a method
which no longer exists. This also adds a test for the from_list_url
function.
2017-10-27 17:41:41 -07:00
Christoph Junghans
95c8ecb6f5
libaec: add v1.0.2 and generic url ( #6017 )
2017-10-27 18:22:27 -06:00
Matthias Diener
45bfcfa30a
Byobu: new package ( #5974 )
2017-10-27 10:43:45 -07:00
Christoph Junghans
f9599c1772
ecp-proxy-apps: add more package ( #6003 )
2017-10-27 08:34:52 -06:00
Christoph Junghans
c97bf0486c
SWFFT: initial commit ( #5953 )
...
* SWFFT: initial commit
* swfft: fix build target
* swfft: add v1.0
* Update package.py
2017-10-27 07:20:29 -06:00
Christoph Junghans
13b41cd53c
comd: add v1.1 ( #5994 )
...
* comd: add v1.1
* Update package.py
* remove serial variant, now ~mpi
* Update package.py
2017-10-27 07:20:18 -06:00
lingnanyuan
222fee1cb3
r-graph: Create new package. ( #5958 )
2017-10-27 08:34:33 +02:00
lingnanyuan
f244653496
r-category: Create new package. ( #5959 )
2017-10-27 08:34:16 +02:00
lingnanyuan
715a679245
r-methodss3: Create new package. ( #5960 )
2017-10-27 08:32:20 +02:00
lingnanyuan
737f9eee5c
r-oo: Create new package. ( #5962 )
2017-10-27 08:31:46 +02:00
lingnanyuan
f676d8f3d7
r-utils: Create new package. ( #5964 )
2017-10-27 08:31:26 +02:00
lingnanyuan
3bb4572e81
r-pfam-db: Create new package. ( #5965 )
2017-10-27 08:27:19 +02:00
lingnanyuan
95ece343c4
r-oligoclasses: Create new package. ( #5966 )
2017-10-27 08:26:25 +02:00
Yifan Zhu
3ea6a11043
r-interactivedisplaybase: created new package ( #5967 )
2017-10-27 08:26:02 +02:00
lingnanyuan
c672b2b191
r-annotationforge: Create new package. ( #5968 )
2017-10-27 08:25:12 +02:00
lingnanyuan
57528fddbb
r-gostats: Create new package. ( #5969 )
2017-10-27 08:24:49 +02:00
Audrey Thoma
835e6107fe
r-mcmcglmm: new package ( #5970 )
2017-10-27 08:24:28 +02:00
Yifan Zhu
7b0fd6510c
r-annotationhub: created new package ( #5972 )
2017-10-27 08:23:25 +02:00
Denis Davydov
c2094a11e3
gnuplot: add 5.2.0 and 5.0.7 ( #5979 )
2017-10-27 08:20:34 +02:00
lingnanyuan
dc8a0e8410
r-deseq2: Create new package. ( #5981 )
2017-10-27 08:16:40 +02:00
lingnanyuan
1de2109a5a
r-agdex: Create new package. ( #5983 )
2017-10-27 08:16:04 +02:00
lingnanyuan
82b1731ded
r-agilp: Create new package. ( #5984 )
2017-10-27 08:15:39 +02:00
lingnanyuan
7c56318cb5
r-aims: Create new package. ( #5987 )
2017-10-27 08:14:55 +02:00
George Hartzell
55b79dca8c
Add info for go@1.9.2 ( #5989 )
...
The go team released 1.9.2 which includes fixes for some things
that 1.9.1 broke:
> ... include fixes to the compiler, linker, runtime, documentation, go command, and the crypto/x509, database/sql, log, and net/smtp packages. They include a fix to a bug introduced in Go 1.9.1 and Go 1.8.4 that broke "go get" of non-Git repositories under certain conditions.
2017-10-27 08:13:33 +02:00
Yifan Zhu
3849401d85
r-annotationfilter: created new package ( #5995 )
2017-10-27 08:09:31 +02:00
Yifan Zhu
0c2a691b1b
r-protgenerics: created new package ( #5998 )
2017-10-27 08:08:16 +02:00
Abhinav Bhatele
ad51e818a7
ecp-proxy-apps: add dependencies ( #5999 )
2017-10-26 19:54:40 -06:00
Christoph Junghans
0b3247c23d
miniamr: bump to v1.4.0 ( #5975 )
2017-10-26 19:51:50 -06:00
Ondřej Čertík
0e464f86bb
Exodus: skip the -G "Unix Makefiles" part ( #5906 )
...
* Exodus: skip the -G "Unix Makefiles" part
The problem is that spack passes -G "Unix Makefiles" into cmake, which normally
works. But in the Exodus package, it is being passed into a bash wrapper
script. In there, the $@ then loses the information about "Unix Makefiles"
being just one argument, and in effect passes -G Unix Makefiles into the cmake
(without quotes), and so cmake only sees -G Unix, and then fails. This is a
known problem with bash with no simple solutions. As a workaround, this patch
skips the first two arguments, i.e., -G and "Unix Makefiles". This makes it
work.
Fixes #5895 .
* Port exodusii to cmake
The cmake options were taken from the cmake-exodus bash script and ported to
spack directly.
* Use variant forwarding to forward the 'mpi'
Now instead of
spack install exodusii~mpi^netcdf~mpi^hdf5~mpi
one can just use
spack install exodusii~mpi
2017-10-26 13:50:18 -06:00
Christoph Junghans
5c09176014
minife: version bump to v2.1.0 ( #5985 )
2017-10-26 11:45:40 -06:00
Abhinav Bhatele
0ff1fe90fa
Laghos: new package ( #5956 )
2017-10-26 09:18:57 -06:00
Abhinav Bhatele
02744141e9
sw4lite: fix build errors and add variants ( #5944 )
...
* sw4lite: fix build errors and add variants
* sw4lite: change linking against blas and lapack
* change order of blas and lapack
* satisfy flake8 requirements
* Update package.py
2017-10-26 09:18:05 -06:00
Jon Rood
18d2fe7647
Customization of the Paraview module file to its nonstandard directory structure ( #5799 )
...
* Add the custom paraview lib directory structure to the library paths in the paraview module file.
* Fixing flake8 issues.
* Checking if lib64 exists for paraview module file generation, else use lib.
* Fixing more flake8 problems I introduced.
2017-10-26 11:12:04 +02:00
Christoph Junghans
a05bbd7104
flang: fixed llvm dep ( #5948 )
...
* flang: fixed llvm dep
* add support for llvm-5
* Update package.py
* Update package.py
2017-10-26 09:34:33 +02:00
Johann Klähn
306f536138
Add option to install clang python bindings to llvm ( #5774 )
2017-10-26 01:46:03 +02:00
Ondřej Čertík
89b0a09de0
Make clang use libc++ by default ( #5943 )
...
Since LLVM 3.9 Clang can use the libc++ library by default using the
CLANG_DEFAULT_CXX_STDLIB cmake configuration variable, without having to
specify the -stdlib=libc++ option on the clang++ command line.
This commit makes clang++ use libc++ by default for LLVM 3.9 and later if the
libcxx variant is on.
Fixes #5942 .
2017-10-25 16:19:32 -06:00
mmwolf
ffb4251666
adding miniTri miniapp ( #5935 )
2017-10-25 15:49:22 -06:00
Omar Padron
dd39862a80
boost: remove duplicate patch ( #5934 )
2017-10-25 12:00:50 -07:00
Jimmy Tang
1f4089a78f
tweak opencv version ( #5623 )
2017-10-25 14:37:40 +02:00
Sergey Kosukhin
c9810f8088
Update for 'netcdf'. ( #5819 )
2017-10-25 14:30:58 +02:00
Audrey Thoma
d839012e00
delly2: new package ( #5820 )
2017-10-25 13:55:13 +02:00
David Hows
05b3178ca4
Zlib gets a 50-60% performance win when compiled with -O2 ( #5838 )
...
Chasing a performance regression has lead me to this change, going from default optimization gives a significant performance win. The sweet spot for zlib is apparently `-O2`, both `-Ofast` and `-O3` are slightly worse (regression is about 3% compared with `-O2) in my testing.
Happy to share my methodology with people so we can benchmark on a wider variety of systems.
2017-10-25 13:53:35 +02:00
Sergey Kosukhin
ce8a698b48
Update for 'eccodes'. ( #5899 )
2017-10-25 13:48:55 +02:00
George Hartzell
5d3a774587
Add package for scalpel@0.5.3 ( #5901 )
...
* Add package for scalpel@0.5.3
Scalpel's a bit of a mess, it expects it's users to just unpack the
tarball, build it in the resulting directory and install that
directory onto their PATH. My install step recapitulates this into
prefix.bin. The alternative was rewiring their scripts (perl), which
use `FindBin` and expect things to be located in the same dir that the
script itself is.
Sigh.
Lightly tested on CentOS 7.
* Flake8 cleanup
* Additional flake8 cleanup
2017-10-25 13:48:11 +02:00
Audrey Thoma
729c88f068
adding perl-bio-perl and dependencies ( #5845 )
...
* perl-bio-perl and dependencies
* minor fixes
* condensing code
* fixing doc error
2017-10-25 13:35:17 +02:00
Sergey Kosukhin
b92ddd72dd
Update for 'cdo'. ( #5947 )
2017-10-25 13:24:19 +02:00
Eric
e2ef033855
bwa: add 0.7.17 ( #5902 )
...
* bwa: add 0.7.17
* bwa: add 0.7.13
2017-10-25 12:21:18 +02:00
George Hartzell
ff031de800
Add old version to bcftools ( #5907 )
...
* bcftools v1.2 and htslib v1.2
* dependency change - only require dependencies for v1.2
2017-10-25 12:20:42 +02:00
Audrey Thoma
9947306c3e
py-xlsxwriter: new package ( #5918 )
2017-10-25 12:19:59 +02:00
George Hartzell
4fb46501af
adding bedtools2 v2.23.0 ( #5911 )
2017-10-25 12:16:10 +02:00
George Hartzell
98c06eae92
Parallel fix sbangs ( #5910 )
...
* Added procedure to edit sbangs of the parallel perl scripts.
* Specify the types of perl dependency
Adding ", type=('build', 'run')" to the dependency declaration to clarify when and how perl is required
* flake8 cleanup
2017-10-25 12:15:10 +02:00
Audrey Thoma
3265008ad2
adding perl-moose and dependencies ( #5912 )
...
* adding perl-moose and dependencies
* added missing dependency
* fixed flake8 errors
2017-10-25 12:07:20 +02:00
Robert Pavel
9e1341a162
Added Hypre Dependency to mfem+hypre ( #5929 )
...
Added missing hypre defendency from mfem's hypre-enabled version
2017-10-25 12:03:50 +02:00
lingnanyuan
acbd6c9f62
r-geneplotter: Create new package. ( #5924 )
2017-10-25 12:01:19 +02:00
lingnanyuan
79b49d44af
r-gridextra: Update version to 2.3 ( #5915 )
2017-10-25 11:50:16 +02:00
Audrey Thoma
f8b90d50de
r-geiger and dependencies ( #5933 )
2017-10-25 11:17:37 +02:00
lingnanyuan
cc51cc0b06
r-rbgl: Create new package. ( #5931 )
2017-10-25 11:17:29 +02:00
Yifan Zhu
f87c426a6c
r-variantannotation: created new package ( #5932 )
2017-10-25 11:17:15 +02:00
lingnanyuan
f1c06dec7c
r-gseabase: Create new package. ( #5930 )
2017-10-25 11:17:00 +02:00
Yifan Zhu
054cc5d361
r-bsgenome: created new package ( #5928 )
2017-10-25 11:16:53 +02:00
Yifan Zhu
6b6d5d20e2
r-lsei: new package ( #5926 )
2017-10-25 11:16:46 +02:00
Yifan Zhu
fc3d484784
r-yarn: created new package ( #5925 )
2017-10-25 11:16:41 +02:00
lingnanyuan
d0a5f73a94
r-formula: Update version to 1.2-2 ( #5923 )
2017-10-25 11:16:34 +02:00
Yifan Zhu
c5447d7818
r-quantro: created new package ( #5922 )
2017-10-25 11:16:20 +02:00
lingnanyuan
05997460f6
r-scales: Update url. ( #5921 )
2017-10-25 11:16:00 +02:00
Yifan Zhu
3216daa905
r-doparallel: added list_url and version 1.0.11 ( #5920 )
2017-10-25 11:15:49 +02:00
lingnanyuan
21799cbe81
r-hmisc: Create new package. ( #5919 )
...
* r-hmisc: Create new package.
* Correct format.
2017-10-25 11:15:40 +02:00
Yifan Zhu
5742ec4fea
r-openssl: changed homepage url to the CRAN package homepage, added list_url and added version 0.9.7 ( #5848 )
2017-10-25 11:12:31 +02:00
Praveen C
5b9de2eaba
Glibc 2.26 does not provide xlocale.h ( #5862 )
2017-10-25 10:39:32 +02:00
Ondřej Čertík
882480fad6
gdbm: pass in proper CPPFLAGS ( #5893 )
...
The problem was that the configure script was not using spack's compiler
wrappers. We now pass the proper compiler wrapper using the CC argument
explicitly.
Fixes #5892 .
2017-10-25 07:09:41 +02:00
Abhinav Bhatele
b47ff33f11
Add a new package for AMG and fix build issues in the amg2013 package ( #5909 )
...
* amg2013: fix build issues
* amg: add new package
* Update package.py
* amg2013: standardize option name
* amg: standardize option names
2017-10-24 21:06:33 -06:00
Ondřej Čertík
39616a2fe1
hypre: make mpi dependency optional ( #5905 )
2017-10-24 18:53:12 -07:00
Robert Pavel
68f7b7863a
Added Spackage for SW4Lite proxy ( #5917 )
...
Added Spackage for C version of SW4Lite proxy. Fortran will follow once
race conditions involving .mod files are resolved
2017-10-24 15:31:05 -06:00
Denis Davydov
31813ef2c7
slepc and petsc version updates ( #5863 )
...
slepc: add 3.8.0
petsc: no longer prefer 3.7.7
2017-10-24 10:57:14 -07:00
Yifan Zhu
8c306b7b83
r-minfi: created new package ( #5887 )
2017-10-24 14:07:45 +02:00
健美猫
37ce53c48f
Add a package: thrust. ( #3729 )
2017-10-24 11:39:38 +02:00
Yifan Zhu
1ee60e7c63
r-nlme: added list_url and version 3.1-131 ( #5890 )
2017-10-24 11:30:49 +02:00
Yifan Zhu
2a2203895a
r-genomicalignments: created new package ( #5785 )
...
* r-genomicalignments: created new package
* r-genomicalignments: using git repo source instead
2017-10-24 11:30:33 +02:00
Yifan Zhu
a68f9dcc26
r-reshape: created new package ( #5889 )
2017-10-24 11:29:56 +02:00
Yifan Zhu
43d39a6b00
r-data-table: added list_url and version 1.10.4-2 ( #5888 )
2017-10-24 11:29:42 +02:00
lingnanyuan
896d4c8d0c
r-mass: Update version to 7.3-47 ( #5885 )
2017-10-24 11:27:04 +02:00
lingnanyuan
cc06112959
r-acepack: Create new package. ( #5884 )
2017-10-24 11:26:37 +02:00
lingnanyuan
b09f0cdbe1
r-latticeextra: Create new package. ( #5883 )
...
* r-latticeextra: Create new package.
* r-latticeextra: Update list_url.
2017-10-24 11:26:20 +02:00
lingnanyuan
01215d705f
r-htmltable: Create new package. ( #5882 )
2017-10-24 11:25:58 +02:00
lingnanyuan
8c0b95c398
r-htmlwidgets: Update verion to 0.9 ( #5881 )
2017-10-24 11:25:42 +02:00
lingnanyuan
22e96a10ad
r-checkmate: Create new package. ( #5880 )
2017-10-24 11:25:24 +02:00
Yifan Zhu
17d94a5b51
r-geoquery: created new package ( #5879 )
...
* r-geoquery: created new package
* r-geoquery: added versioned dependency on r
2017-10-24 11:25:02 +02:00
lingnanyuan
25d38fe077
r-knitr: Update version to 1.17. ( #5878 )
2017-10-24 11:24:45 +02:00
Yifan Zhu
bba655d6d7
r-httr: added list_url and version 1.3.1 ( #5877 )
2017-10-24 11:24:29 +02:00
lingnanyuan
d4d44f0c63
r-rcpparmadillo: Create new package. ( #5875 )
2017-10-24 11:24:16 +02:00
Yifan Zhu
eeb1edd8e5
r-curl: added list_url and version 3.0 ( #5874 )
2017-10-24 11:23:54 +02:00
lingnanyuan
859b9972d3
r-yaml: Update version to 2.1.14 ( #5856 )
2017-10-24 11:23:38 +02:00
lingnanyuan
ae578069bd
r-formatr: Update version to 1.5 ( #5855 )
2017-10-24 11:23:17 +02:00
lingnanyuan
050b753bb7
r-crayon: Update version to 1.3.4 ( #5854 )
2017-10-24 11:23:00 +02:00
lingnanyuan
764b7a7ad1
r-sourcetools: Create new package. ( #5853 )
2017-10-24 11:22:42 +02:00
lingnanyuan
4b50598252
r-testit: Update version to 0.7 ( #5852 )
2017-10-24 11:22:23 +02:00
lingnanyuan
6b87875d81
r-markdown: Update version to 0.8. ( #5851 )
2017-10-24 11:22:05 +02:00
Yifan Zhu
ab96705f05
r-base64: created new package ( #5850 )
2017-10-24 11:21:48 +02:00
Yifan Zhu
f814e9bba1
r-illuminaio: created new package ( #5849 )
2017-10-24 11:21:31 +02:00
lingnanyuan
7a176ca89e
r-evaluate: Update version to 0.10.1. ( #5847 )
...
* r-evaluate: Update version to 0.10.1.
* r-evaluate: update list_url.
2017-10-24 11:20:47 +02:00
lingnanyuan
420048350f
bioconductor update ( #5786 )
...
* r-a4: Add r dependency and update url.
* r-a4base: Add r dependency and update url.
* r-a4classif: update url and add r dependency.
* r-a4core: Update url and add r dependency.
* r-a4preproc: Update url and add r dependency.
* r-a4reporting: Update url and add r dependency.
* r-abaenrichment: Update url and add r dependency.
* r-absseq: Update url and add r dependency.
* r-acgh: Update url and add r dependency.
* r-acme: Update url and add r dependency.
* r-adsplit: Update url and add r dependency.
* r-affxparser: Update url and add r dependency.
* r-affycomp: Update url and add r dependency.
* r-affycompatible: Update url and add r dependency.
* r-affycontam: Update url and add r dependency.
* r-annaffy: Update url and add r dependency.
* r-annotate: Update url and add r dependency.
* r-annotate: Update url and add r dependency.
* r-annotationdbi: Update url and add r dependency.
* r-genefilter: Update url and add r dependency.
* r-mlinterfaces: Update url and add r dependency.
* r-limma: Update url and add r dependency.
* r-multtest: Update url and add r dependency.
* r-a4classif: Correct format.
* r-affycomp: Correct error.
2017-10-24 11:19:19 +02:00
Yifan Zhu
f9f0c1472f
r-siggenes: new package ( #5831 )
...
* r-siggenes: created new package
* deleted extra indent
2017-10-24 11:14:04 +02:00
lingnanyuan
cea33af464
r-affyrnadegradation: Create new package. ( #5830 )
2017-10-24 11:13:53 +02:00
lingnanyuan
2ede483149
r-affyqcreport: Create new package. ( #5829 )
2017-10-24 11:13:44 +02:00
Yifan Zhu
edac742f84
r-nor1mix: created new package ( #5828 )
2017-10-24 11:13:04 +02:00
lingnanyuan
46b385761d
r-affyplm: Create new package. ( #5827 )
2017-10-24 11:12:56 +02:00
lingnanyuan
2c5b3a2268
r-affypdnn: Create new package. ( #5826 )
2017-10-24 11:12:47 +02:00
Yifan Zhu
6fd0030acb
r-beanplot: created new package ( #5825 )
...
* r-beanplot: created new package
* correct according to flake8
2017-10-24 11:12:15 +02:00
Aaron Fisher
204217f7c1
Updated external package versions. ( #5833 )
2017-10-24 11:10:59 +02:00
Yifan Zhu
968144f1c5
r-bumphunter: new package ( #5824 )
...
* r-bumphunter: created new package
* r-bumphunter: added description
2017-10-24 11:09:38 +02:00
Sergey Kosukhin
161dca6d5d
Update for 'hdf5'. ( #5790 )
...
* Refactoring for 'hdf5'.
* Remove 'unsupported' variant.
2017-10-24 11:09:08 +02:00
Michael Kuhn
c7ac4e3774
go: Update to 1.9.1 ( #5868 )
2017-10-24 11:02:33 +02:00
Todd Gamblin
5449884b2e
Fix bare 'except:' to placate errors in new flake8 version.
...
- fixes E722 errors from latest version of flake8
- requires us to not use 'bare except:' and catch BaseException instead
2017-10-24 10:05:36 +02:00
Todd Gamblin
0bb1eb32f2
fix bugs found with stricter flake8 rules
...
- When you don't use wildcards, flake8 will find places where you used an
undefined name.
- This commit has all the bugfixes resulting from this static check.
2017-10-24 10:05:36 +02:00
Todd Gamblin
7dd79094b0
remove wildcards from make spack core and packages
...
- This removes all wildcard imports EXCEPT `from spack import *` in packages
2017-10-24 10:05:36 +02:00
Todd Gamblin
beab0cb92e
add newlines at end of some package files
2017-10-24 10:05:36 +02:00
Mark Grondona
328dc3d140
jansson: enable shared library ( #5857 )
...
Jansson builds only a static library by default, which is probably
not what most users want. Add Cmake args required to build a shared
library and enable those via a default 'shared' variant of the
package.
2017-10-23 13:32:51 +02:00
jiseung
969c8b177f
new package: hpgmg ( #4888 )
...
* new package: hpgmg
* removed build and changed extend() to append()
* changes based on comments
* pep8 compliant
* addressed rest of comments
* trigger checks
* changed from fe_fv to two boolean variants
* fixed compilation issues
* cleared up ambiguities in solver variants
* removed +mpi condition
* changes based on review
2017-10-20 17:34:55 -07:00
George Hartzell
c9d9901e43
perl: add old version ( #5844 )
2017-10-20 16:18:24 -07:00
Christoph Junghans
2e1a96f262
xsbench: add v14 ( #5835 )
2017-10-20 08:52:17 +02:00
