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4537 commits

Author SHA1 Message Date
Yifan Zhu
350624a231 r-dorng: created new package (#5740) 2017-10-13 07:47:01 -06:00
Yifan Zhu
9f3e055e8b r-stringr: added list_url and version 1.2.0 (#5738) 2017-10-13 07:46:29 -06:00
Yifan Zhu
525b69bbad r-stringi: added list_url and version 1.1.5 and 1.1.3 (#5737) 2017-10-13 07:45:26 -06:00
Yifan Zhu
0b117a03c6 r-summarizedexperiment: created new package (#5734) 2017-10-13 07:45:05 -06:00
Yifan Zhu
501ebe6706 r-yaqcaffy: added list_url and versioned dependency on r (#5730) 2017-10-13 07:44:26 -06:00
Denis Davydov
65f12c8160 slepc: refine version constraints for petsc 3.8 (#5752) 2017-10-13 07:11:17 -06:00
Denis Davydov
22ef8efce9 openblas: remove extra develop version (#5750) 2017-10-13 12:10:05 +02:00
Denis Davydov
b182e2334d gettext: fix prefix (#5749) 2017-10-13 10:52:55 +02:00
Brian Van Essen
bd185b8146 Lbann flags (#5747) 
* Fixed the datatype flag in the LBANN package.  Also added develop
version to OpenBLAS.

* Fixed where the datatype flag should be set.
 2017-10-12 20:23:38 -06:00
Yifan Zhu
f2a6685d8c r-gcrma: added versioned dependency on r (#5670) 2017-10-12 16:18:30 -06:00
Yifan Zhu
d4906169e0 r-simpleaffy: added versioned dependency on r (#5673) 2017-10-12 16:18:15 -06:00
Satish Balay
59163f9750 petsc: add in maintainers (#5729) 2017-10-12 15:09:47 -06:00
David Hows
8ff8b7476c Add the option for a versioned layout to boost (#5709) 2017-10-12 12:51:39 -06:00
Audrey Thoma
36ed96e7dd kaks-calculator: new package (#5725) 
* kaks-calculator: new package

* kaks-calculator: new package

* fixing homepage
 2017-10-12 12:47:11 -06:00
Satish Balay
98c2184bd3 petsc: update to latest 3.8 version [and include 3.7.7] (#5723) 
Also fix flake8 warning "import os should be before import sys"
 2017-10-12 12:46:00 -06:00
Jon Rood
c0b2e7db73 Add OpenFAST package (wind turbine simulation tool). (#5662) 
* Add OpenFAST package (wind turbine simulator).
* Adding maintainer to openfast package.
* Fixing copyright date.
 2017-10-12 11:42:51 -07:00
Denis Davydov
1b53e82348 various fixes for macOS high sierra (#5647) 
* various fixes for macOS high sierra

* add macOS_version() helper function

* flake8 fixes

* update oce and trilinos

* fix bison
 2017-10-12 11:41:57 -07:00
Carlos Bederián
db149876a4 samtools: add version 1.6 + some fixes (#5715) 
* htslib: add version 1.6

* samtools: add version 1.6, remove zlib dependency

* bcftools: add version 1.6, switch to using standalone htslib
 2017-10-12 10:08:31 -06:00
Audrey Thoma
87c65fafa9 minimap2: new package (#5722) 2017-10-12 10:07:42 -06:00
David Hows
90cd075277 Initial version of libpcap (#5710) 
Add a package script for libpcap with the current version (1.8.1)
 2017-10-12 07:00:21 -06:00
Yifan Zhu
e807397074 r-affy: added versioned dependency on r (#5660) 2017-10-11 19:49:48 -06:00
Yifan Zhu
36eba3bf58 r-affyio: added versioned dependency on r (#5661) 2017-10-11 19:49:28 -06:00
Yifan Zhu
db0fec4d09 r-biocinstaller: added versioned dependency on r (#5663) 2017-10-11 19:49:08 -06:00
Yifan Zhu
4e8ac1d525 r-matrixstats: created new package (#5682) 2017-10-11 19:48:39 -06:00
Yifan Zhu
5e41ad6fed r-biocgenerics: added version 0.22.1 and added versioned dependency on r (#5683) 2017-10-11 19:48:19 -06:00
Yifan Zhu
8d48f07de1 r-genomeinfodbdata: added versioned dependency on r (#5685) 2017-10-11 19:48:00 -06:00
Yifan Zhu
a04e95a492 r-genomeinfodb: created new package (#5695) 2017-10-11 19:47:03 -06:00
Yifan Zhu
dc95dddd61 r-genomicranges: added new package (#5697) 2017-10-11 19:45:03 -06:00
Yifan Zhu
c93ecda872 r-futile-options: created new package (#5699) 2017-10-11 19:43:53 -06:00
Yifan Zhu
4af446d7f4 r-lambda-r: created new package (#5700) 2017-10-11 19:43:33 -06:00
Yifan Zhu
f8db73d567 r-futile-logger: created new package (#5701) 2017-10-11 19:43:15 -06:00
Yifan Zhu
01e104dfcb r-rsamtools: created new package (#5702) 2017-10-11 19:42:55 -06:00
Yifan Zhu
670463e95a r-biocparallel: created new package (#5703) 2017-10-11 19:42:25 -06:00
Yifan Zhu
e08e7af34e r-delayedarray: created new package (#5704) 2017-10-11 19:42:04 -06:00
Yifan Zhu
9a2ef4c4b3 r-biomart: added versioned dependency on r (#5666) 2017-10-11 19:41:08 -06:00
George Hartzell
124bdfb910 Strelka depends on boost 1.56.0 *or newer* (#5690) 
Relax/correct the constraint on the version of boost used
by Strelka to match the docs.
 2017-10-11 17:21:26 -06:00
Denis Davydov
35a62f715b dealii: minor fixes (#5687) 
* dealii: fix minor bug in Assimp config

* dealii: request sundials without pthreads
 2017-10-11 15:09:39 -06:00
Christoph Junghans
cfc13dec9f Add a bundle package for the ECP proxy applications suite (#5689) 
* Add a bundle package for the ECP proxy applications suite

* Update package.py
 2017-10-11 13:39:30 -06:00
健美猫
9e95e8394e Add a package: dmlc/mxnet. (#3579) 
* Add dmlc/mxnet packags.

* Build mxnet+cuda+opencv with GCC-4.8.5 and GCC-5.4.0.

* Build mxnet version 0.10.0, 0.10.0.post1 and 0.10.0.post2.

* Add component version constrain for mxnet 0.10.0.x .

* Go through flake8.

* Replace commit hash with commit date as package version.

* Go throught Travis-CI.

* Update submodule version for 0.10.0.post2.

* Add openmp variant for dmlc-core and mxnet.

* Refine variant handling.

* Fix filter_file for dmlc-core.

* Cut long strings into multiple lies due to PEP8 requirements.

* Fix for PEP8.

* Add CUB_INCLUDE.

* Add py-mxnet: Python binding for MXNet.

* Remove distutils.dir_util.

* Add the profiler variant for mxnet.

* Add a shared variant for nnvm.

* Set USE_OPENMP to OFF by default.

* Fix flake8 errors.

* Fix flake8 issues.

* flake8 issues again.
 2017-10-10 13:56:26 -07:00
Christoph Junghans
ef822453b9 Adding flang - a llvm based Fortran compiler (#5459) 
* flang: initial commit

* flang: added symlink to clang's flang

* add flang wrapper

* flang wrapper: inject rpath as well

* flang wrapper: PATH -> -B
 2017-10-10 13:52:31 -07:00
Christoph Junghans
88b515ede8 ninja: add v1.8.2 (#5625) 2017-10-10 12:50:56 -07:00
Massimiliano Culpo
a3bbe066b3 plumed: reworked patching applications, added new version (#5680) 
closes #5506

The application of patches to upstream executables has been reworked
according to the suggestions of the main developer in #5506. In
particular we are not maintaining a dictionary that maps plumed
versions to the versions of patchable executables, and we are using a
non-interactive command to patch applications.

All the comments on substituting plumed at run-time do not apply here,
since we use RPATH and we want to maintain a 1:1 relationship between
the DAG hash and the plumed library used.
 2017-10-10 12:35:53 -07:00
Audrey Thoma
e3053d7425 snap-korf: new package (#5589) 2017-10-10 11:09:31 -07:00
Jon Rood
f2b49d8f66 Adding openfast variant to nalu. (#5675) 2017-10-09 20:10:47 -06:00
lingnanyuan
35583f48f4 r-adsplit: Create new package and update version for its dependencies. (#5640) 
* r-adsplit: Create new package.

* r-rlang: Update version.

* r-s4vectors: Update version.
 2017-10-09 17:10:29 -06:00
Audrey Thoma
a8cd92a2e4 switching downloads to git (#5659) 2017-10-09 17:07:13 -06:00
lingnanyuan
196b82f2c7 r-affycompatible: Create new package. (#5664) 2017-10-09 17:05:53 -06:00
lingnanyuan
ef1f71447e r-affydata: Create new package. (#5665) 2017-10-09 17:05:21 -06:00
lingnanyuan
1f05e9ae58 r-affycontam: Create new package. (#5668) 2017-10-09 17:04:51 -06:00
George Hartzell
ab2c7573c1 strelka: new package (#5632) 
* Add package for strelka@2.8.2

* Fix flake8 complaints
 2017-10-09 17:02:44 -06:00