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4668 commits

Author SHA1 Message Date
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