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Author SHA1 Message Date
Yifan Zhu
3c0e799a51 r-limma: added version 3.32.7 (#5558) 2017-09-29 16:29:41 -06:00
Jon Rood
ebbdde9625 Masa requires python if +python. (#5547) 2017-09-29 16:14:12 -06:00
lingnanyuan
756fb83f04 r-a4classif: new package. (#5557) 2017-09-29 16:06:27 -06:00
lingnanyuan
17b8f6b818 r-yaml: Correct url (#5550) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-yaml: Correct url.
 2017-09-29 16:05:55 -06:00
Yifan Zhu
7c87cb1ad1 r-downloader: created new package (#5556) 2017-09-29 16:05:30 -06:00
lingnanyuan
f9e33e9b59 r-mlinterfaces: new package. (#5555) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-mlinterfaces: Create new package.
 2017-09-29 15:34:44 -06:00
Yifan Zhu
06a6c6a399 r-biomart: created new package (#5554) 2017-09-29 15:33:40 -06:00
lingnanyuan
18029f5f47 r-threejs: Correct url. (#5553) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-threejs: Correct url.
 2017-09-29 15:33:05 -06:00
Jon Rood
d19eb152c8 Adding new Trilinos version and updating Nalu to utilize it. (#5552) 2017-09-29 15:31:15 -06:00
lingnanyuan
e1f33bd903 r-hwriter: new package. (#5549) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-hwriter: Create new package.
 2017-09-29 15:29:26 -06:00
lingnanyuan
211f731065 r-gbm: new package. (#5548) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-gbm: Create new package.
 2017-09-29 15:29:11 -06:00
lingnanyuan
4cc1ff5ce8 r-htmlwidgets: Update version to 0.8. (#5551) 2017-09-29 14:28:48 -07:00
lingnanyuan
89b30bea7f r-a4preproc: Create new package. (#5499) 2017-09-29 15:27:20 -06:00
Yifan Zhu
a63fdc8f35 r-dbi: updated to version 0.7 (#5537) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-dbi: Create new package.

* r-dbi: modified according to flake8

* Update package.py

* Update package.py
 2017-09-28 22:14:56 -06:00
lingnanyuan
aab68aaecf r-gdata: Update version to 2.18.0 (#5495) 2017-09-28 18:13:06 -07:00
Mark C. Miller
e851d15974 fixing tag name for development branch (#5496) 2017-09-28 18:12:02 -07:00
Yifan Zhu
aee44efada r-biostrings: created new package (#5498) 2017-09-28 18:11:28 -07:00
Yifan Zhu
b455fa2a7b r-gcrma: created new package (#5500) 2017-09-28 18:11:02 -07:00
Yifan Zhu
e42fd90df2 r-yaqcaffy: created new package (#5538) 2017-09-28 18:02:58 -07:00
Jon Rood
5e3024368e Add metaphysicl package (#5539) 
* Adding package Metaphysicl.

* Removing list_url from metaphysical package.
 2017-09-28 18:02:07 -07:00
Jon Rood
90e4b56362 Adding masa package. (#5541) 2017-09-28 18:01:38 -07:00
Yifan Zhu
6d63be9eb6 r-rlang: created new package (#5535) 2017-09-28 16:07:13 -06:00
Christoph Junghans
337256ee32 tycho2: initial commit (#5196) 2017-09-28 14:48:54 -07:00
Mark Olesen
aff6148116 Restrict openfoam to using openmpi+thread_multiple (partially resolves #5428) (#5479) 
- latest version requires openmpi+thread_multiple for collated output.
 2017-09-28 14:42:14 -06:00
Michael Kuhn
97bc86d617 snappy: Build shared library by default (#5534) 2017-09-28 14:18:50 -06:00
lingnanyuan
aa40509fa0 r-ggvis: Update version to 0.4.3 (#5532) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-ggvis: Update version to 0.4.3

* Update package.py

* Update package.py
 2017-09-28 13:13:47 -06:00
lingnanyuan
0962088776 r-dplyr: Update version to 0.7.3 (#5531) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-dplyr: Update version to 0.7.3

* Update package.py

* Update package.py
 2017-09-28 13:09:30 -06:00
Michael Kuhn
ac98e0978a ncl: Add tcsh dependency (#5195) 
All ncl scripts hardcode /bin/csh, so fix them up.
 2017-09-28 12:51:04 -06:00
Michael Kuhn
17be89c210 tcsh: New package (#5194) 
The patches are taken from the Fedora package.
 2017-09-28 12:50:52 -06:00
lingnanyuan
0bc3578dac r-annaffy: new package. (#5414) 
* r-annaffy: Create New Package.

* r-annaffy: Create new package.

* r-go-db: Create new package.

* r-kegg-db: Create new package.

* r-annaffy: Correct indentation.

* r-go-db: Correct indentation.

* r-kegg-db: Correct format.

* r-kegg-db: Correct format.

* r-go-db: Correct format.

* r-annaffy: Correct format.
 2017-09-28 12:49:31 -06:00
Audrey Thoma
3f44eb0179 fastq-screen: new package (#5431) 
* fastq-screen: new package

* fixing descriptions and previously made packages' old copyright date

* added wrong perl package after change
 2017-09-28 12:48:31 -06:00
Brian Homerding
0ce93d7333 Added hacckernels package (#5533) 2017-09-28 12:46:26 -06:00
lingnanyuan
d61e92b439 r-r6: Update version to 2.2.2 (#5529) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-r6: Update version to 2.2.2
 2017-09-28 12:46:11 -06:00
lingnanyuan
c0e1b1f68e r-shiny: update version to 1.0.5 (#5530) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-shiny: Update version to 1.0.5
 2017-09-28 11:31:27 -06:00
lingnanyuan
a613244602 r-htmltools: Update version to 0.3.6 (#5528) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-htmltools: Update version to 0.3.6
 2017-09-28 11:31:16 -06:00
lingnanyuan
0c385e94e6 r-httpuv: Update version to 1.3.5 (#5527) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-httpuv: Update version to 1.3.5
 2017-09-28 11:30:57 -06:00
lingnanyuan
38ea408126 r-rcpp: Update version to 0.12.13 (#5526) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-rcpp: Update version to 0.12.13

* r-rcpp: Correct url.
 2017-09-28 11:30:25 -06:00
Kelly (KT) Thompson
4e4247dd18 Provide a new Perl package 'cloc'. (#5525) 
+ Count, or compute differences of, physical lines of source code in the
  given files (may be archives such as compressed tarballs or zip files)
  and/or recursively below the given directories.
 2017-09-28 11:30:08 -06:00
lingnanyuan
e101665e5e r-jsonlite: Update version to 1.5 (#5524) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-jsonlite: Update version to 1.5
 2017-09-28 11:28:49 -06:00
lingnanyuan
4d445f8436 r-rda: new package. (#5523) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-rda: Create new package.
 2017-09-28 11:28:29 -06:00
Mark Olesen
cd825baee9 - build paraview without qt when osmesa is specified. (#5480) 
- new paraview version (5.4.1 from August)
 2017-09-27 22:32:10 -06:00
lingnanyuan
ab21d268be r-sfsmisc: new package. (#5516) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-sfsmisc: Create new package.

* r-sfsmisc: Correct format.
 2017-09-27 22:16:02 -06:00
Robert Pavel
b681146875 Added spackage for branson (#5520) 
Added spackage for branson proxy for monte carlo
 2017-09-27 21:50:07 -06:00
Gregory Lee
16bd1449be added qt creator version 4.4.0 (#5518) 2017-09-27 21:49:33 -06:00
lingnanyuan
d5fcbab8de r-varselrf: new package. (#5515) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-varselrf: Create new package.
 2017-09-27 21:48:22 -06:00
lingnanyuan
97208d9888 r-pamr: new package (#5514) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-pamr: Create new package.
 2017-09-27 21:48:04 -06:00
lingnanyuan
51e99c5fde r-rocr: new package. (#5513) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-rocr: Create new package.
 2017-09-27 21:47:47 -06:00
lingnanyuan
e7c0e12256 r-a4core: new package. (#5512) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-a4core: Create new package.

* r-a4core: Correct format.
 2017-09-27 21:47:12 -06:00
Yifan Zhu
98bb213fe2 r-simpleaffy: created new package (#5510) 2017-09-27 21:46:53 -06:00
Robert Pavel
48066a808e ExaMPM (#5509) 
* Added ExaMPM Spackage

* Removed template text
 2017-09-27 21:46:32 -06:00
Robert Pavel
2942ddc1e0 Added Support for BML 1.2.2 (#5502) 
* Added Support for BML 1.2.2

* Added checksums

* Update package.py
 2017-09-27 21:46:14 -06:00
Robert Pavel
e4f4f9a6e5 Added shards and intrepid(2) to trilinos (#5481) 
Added support for shards, intrepid, and intrepid2 variants to trilinos
spackage
 2017-09-27 21:41:53 -06:00
Robert Pavel
aa2a403536 Added CoEVP Spackage (#5485) 
* Added CoEVP Spackage

Added spackage for baseline (mpi, no other dependencies) CoEVP

* coevp: add more variants

* tag as proxy-app
 2017-09-27 21:41:34 -06:00
Sheng Di
3be81a0b10 SZ: add version 1.4.11 (#5517) 2017-09-27 16:30:43 -07:00
Christoph Junghans
f27aad68bf flann: fix build for 1.8.1 (#5508) 
* Update url_for_version for versions 1.8.1 and earlier
* Add python dependency when +python is enabled
 2017-09-27 14:39:33 -07:00
Christoph Junghans
83ab062583 lammps: add user-omp package (#5486) 
* Simplify cmake arg generation
* Set -DFFT when kspace variant is enabled
 2017-09-27 12:46:58 -07:00
Ken Raffenetti
c242165ebd Additional MPICH configs (#5259) 
* Add support for building develop version from git
* Add device and netmod variants
 2017-09-27 10:50:05 -07:00
lingnanyuan
90dd5e2932 r-gplots: Create New Package. (#5494) 
* r-gplots: Create New Package.

* r-gplots: Correct format.
 2017-09-27 10:20:17 -06:00
Michael Kuhn
ed6003b514 libbson, libmongoc: Update to 1.8.0 (#5478) 2017-09-27 10:19:10 -06:00
Yifan Zhu
df1606e84e r-rcurl: created new package (#5492) 2017-09-26 17:49:54 -06:00
lingnanyuan
618d3add4f r-annotate: new package. (#5490) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-annotate: Create new package.

* r-annotate: Create new package.
 2017-09-26 15:39:34 -06:00
zenln
c7f8405636 Autodock vina: spec (#5333) 
* Autodock vina: spec

* Adding comment to patch. The implemnetation of boost is version dependent on older boost replacing depecrated function of boost.

* Adding in boost version dependency
 2017-09-26 14:44:21 -06:00
Jim Galarowicz
95ff37309a Add ability to build llvm-openmp-ompt alone, with gnu compilers and use the resulting ompt interface in cbtf-krell and openspeedshop to gather openmp specific performance information. (#5288) 
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Trim comments to fit more concisely.

* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.

* Add ability to build llvm-openmp-ompt alone, with gnu compilers and use the resulting ompt interface in cbtf-krell and openspeedshop to gather openmp specific performance information.

* Fix flake8 errors.

* Fix flake8 errors - stage 2.

* Fixes based on reviewer suggestions and comments.

* Use build_type variant to set the build type and allow changing of the type.

* Fix missing comma in cmake_arg list, found on another test machine.
 2017-09-26 14:15:37 -06:00
Christoph Junghans
e3e030cf76 astyle: homepage dead, use mirror (#5483) 2017-09-26 13:03:34 -06:00
Michael Kuhn
86d681be6e snappy: Update to 1.1.7 (#5477) 
Convert to CMakePackage and add a pkg-config file (otherwise libmongoc's
pkg-config file does not contain all required flags).
 2017-09-26 11:00:21 -06:00
Michael Kuhn
733965b3c6 autoconf, automake: Add missing perl dependency (#5187) 
* autoconf, automake: Add missing perl dependency

* automake: Add 1.15.1
 2017-09-26 08:10:22 -06:00
Michael Kuhn
60f8621704 Missing perl dependencies (#5204) 
* glib: Add missing perl dependency

* shared-mime-info: Add missing perl dependency

* libx11: Add missing perl dependency

* likwid: Add missing perl dependency
 2017-09-26 07:27:28 -06:00
lingnanyuan
f3152a5600 r-limma: new package. (#5468) 
* r-limma: Create New Package.

* pr-quantities: add version & py-numpy conflict (#5307)

* r-limma: Create new package.

* r-limma: Correct format.

* Update package.py
 2017-09-25 19:55:03 -06:00
Yifan Zhu
9b2c9bb699 r-affy: created new package (#5471) 2017-09-25 16:57:56 -06:00
lingnanyuan
34d4131284 r-genefilter: New package. (#5467) 
* r-genefilter: Create New Package.

* r-genefilter: Create new package.

* r-genefilter: Correct format.

* Update package.py
 2017-09-25 16:57:17 -06:00
Yifan Zhu
111c216fb7 r-xml: updated url and added version 3.98-1.9 (#5466) 
* r-xml: updated url and added version 3.98-1.9

* Update package.py
 2017-09-25 16:46:01 -06:00
lingnanyuan
8f0fbb4e11 r-multtest: new package. (#5469) 
* r-multtest: Create New Package.

* pr-quantities: add version & py-numpy conflict (#5307)

* r-multtest: Create new package.

* r-multtest: Correct format.
 2017-09-25 16:45:21 -06:00
lingnanyuan
fefb668dcb r-plogr: new package. (#5443) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-plogr:Create new package.

* r-plogr: Correct format.
 2017-09-25 16:42:03 -06:00
lingnanyuan
fafd240c30 r-glmnet: update version. (#5470) 
* r-glmnet: Create New Package.

* pr-quantities: add version & py-numpy conflict (#5307)

* r-glmnet: Update version to 2.0-13

* r-matrix: Update version to 1.2-11

* r-lattice: Update version to 0.20-35.
 2017-09-25 16:39:41 -06:00
lingnanyuan
33adb08672 r-pkgconfig: new package. (#5441) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-pkgconfig: Create new package.

* r-pkgconfig: Correct format.

* r-pkgconfig: Correct format.
 2017-09-25 16:38:45 -06:00
lingnanyuan
eb4ad328ee r-bit64: new package. (#5437) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-bit64: Create new package.

* r-bit64: Correct format.
 2017-09-25 16:38:18 -06:00
lingnanyuan
23235cf3e3 r-annotationdbi: new package (#5408) 
* r-annotationdbi: Create New Package.

* r-iranges: Create new package.

* r-s4vectors: Create new package.

* r-annotationdbi: Create new package.

* r-s4vectors: Delete file.

* r-annotationdbi: Correct format.

* r-iranges: Correct format.
 2017-09-25 16:37:31 -06:00
lingnanyuan
f94b23a249 r-blob: new package. (#5438) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-blob: Create new package.

* r-blob: Correct format.
 2017-09-25 14:41:18 -06:00
Todd Gamblin
13b61913da patch py-mccabe and py-flake8 to not require pytest-runner for install (#5427) 
- Filter the pytest-runner dependency out of setup.py in py-mccabe and
  py-flake8
 2017-09-25 12:46:47 -07:00
Cyrus Harrison
1348fd5648 update for conduit 0.3.0 release (#5421) 
* update for conduit 0.3.0 release

* use mpicxx

* Update package.py
 2017-09-25 12:25:40 -06:00
Axel Huebl
28dd6b378c Fix Protobuf URLs (#5373) 
The default implementation of Package.fetch_remote_versions will take
a URL like https://github.com/google/protobuf/archive/ and automatically
search https://github.com/google/protobuf/releases/ for new package
versions. In the case of protobuf the release/ path contains release
artifacts for a version and the archive/ path contains the desired
source. Since both are associated with the version, and
Package.fetch_remote_versions only stores one URL for a given version,
the two paths are in conflict; previously the URL returned for a
given version was arbitrarily chosen between the two paths. This
updates the definition for the Protobuf package to always search for
URLs in https://github.com/google/protobuf/archive/
 2017-09-25 10:47:55 -07:00
Christoph Junghans
64311e8510 lammps: add support of latte package (#5446) 2017-09-25 09:39:29 -07:00
George Hartzell
e947a0b152 Add info for lmod@7.7 and lmod@7.6.14 (#5450) 
Lightly tested on CentOS 7
 2017-09-25 07:31:43 -06:00
Denis Davydov
330211468a add assimp package. link against it in dealii (#5463) 2017-09-25 06:58:13 -06:00
George Hartzell
99cefcc955 New version for mosh1.3.2 (#5448) 
Required an update to the protobuf digest value, which seems to
be amongst the set creamed by GitHub's change.
 2017-09-24 15:12:35 -06:00
Andrey Prokopenko
6168b7fda8 llvm: patch lldb for gcc-7 (#5239) 2017-09-24 10:24:36 +02:00
Denis Davydov
8db69de258 hdf5: fix macOS build by not using numactl (#5458) 2017-09-23 22:34:00 -06:00
Christoph Junghans
40777e44e2 parsplice: add version 1.1 (#5461) 2017-09-23 20:28:40 -07:00
Denis Davydov
7f84de52a0 blas_lapack: add multithreading variant consistent in all implementations. (#5340) 
* blas_lapack: add multithreading variant

* elemental: update

* intel-mkl: extend to macOS

* rename multithreading to threads

* intel-mkl: avoid long lines

* intel-mkl: make one install error a conflict

* openblas: fix a minor bug in the test
 2017-09-23 13:27:42 -07:00
lingnanyuan
bf2f96ce78 r-rsqlite: Update version to 2.0. (#5444) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-rsqlite: Update version to 2.0
 2017-09-23 15:02:27 +00:00
lingnanyuan
c3a8f10bf9 r-bh: update version. (#5442) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-bh: Update version to 1.65.0-1
 2017-09-23 15:01:35 +00:00
lingnanyuan
8e2351f96c r-memoise: update version. (#5440) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-memoise: Update version to 1.1.0
 2017-09-23 15:00:50 +00:00
lingnanyuan
9fdcc147a7 r-tibble: update version. (#5439) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-tibble: Update version to 1.3.4
 2017-09-23 15:00:02 +00:00
lingnanyuan
c6a3f4cf9b r-bit: new package. (#5436) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-bit: Create new package.
 2017-09-23 14:59:09 +00:00
lingnanyuan
debc492032 r-assertthat: update version to 0.2.0 (#5435) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-assertthat: Update version to 0.2.0
 2017-09-23 14:58:53 +00:00
Yifan Zhu
72bb53c018 r-preprocesscore: created new package (#5434) 2017-09-23 14:58:24 +00:00
Yifan Zhu
6134e94ede r-affyio: created new package (#5433) 2017-09-23 14:58:06 +00:00
Yifan Zhu
d2c65247b0 r-xvector: created new package (#5432) 2017-09-23 14:57:31 +00:00
Denis Davydov
4c20d9917e superlu-dist: fix has after 09/17/2017 update (#5457) 2017-09-23 12:50:02 +00:00
George Hartzell
d12f52b37a tmux: add version 2.5 (#5449) 2017-09-22 19:30:47 -07:00