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Author SHA1 Message Date
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
George Hartzell
6e20dd61c0 Ack: add version 2.18 (#5445) 2017-09-22 19:30:12 -07:00
George Hartzell
e43ea22e45 Add info for httpie@0.9.9 (#5451) 
Lightly tested on CentOS 7.
 2017-09-23 00:40:22 +00:00
George Hartzell
6ac28c1daa Add info for lftp@4.8.1 (#5452) 
Lightly tested on CentOS 7.
 2017-09-23 00:39:49 +00:00
George Hartzell
315d844ab7 Update git to @2.14.1, requires pcre+jit variant (#5430) 
Update the git package to git@2.14.1.

This requires a pcre that has been built with `--enable-jit`, so this
adds a variant to pcre to support that and arranges so that git versions
before 2.14 depend on pcre and git 2.14 and after depend on pcre+jit.
 2017-09-22 16:43:45 -07:00
George Hartzell
fd552ab2b9 git-lfs: add 2.2.1 and 2.3.0 (#5429) 2017-09-22 16:36:57 -07:00
George Hartzell
e176c3a3c5 emacs: add version 25.3 (security update) (#5447) 
25.3 is a security update. Info here:
https://lists.gnu.org/archive/html/info-gnu/2017-09/msg00006.html

Build both +X and ~X on CentOS 7 and lightly tested.
 2017-09-22 16:34:59 -07:00
Massimiliano Culpo
f1fbcfa971 plumed: fixed possible linking issue (#5425) 
Due to the logic in configure.ac, we may be using both the system
linker (LD_RO='ld -r -o') and the linker tied to the compiler (LD=$CXX).
This may produce weird link-time errors when the two executables are
not the same.

The PR works around the issue disabling 'ld -r'
 2017-09-22 21:14:53 +02:00
Howard Pritchard
a646ec1fff PMIx: add PMIx package to Spack (#5426) 
Open MPI has been relying on versions of PMIx since the 2.0.0
release.  Although the embedded version can be used, it makes
more sense long term for Spack to know about the PMIx package,
and to build Open MPI against PMIx as an external package.

There are other software components that may eventually be
reliant on PMIx including MPICH, GASNet, the OpenSHMEM reference
implementation, etc.

This is also partly motivated by the desire to have ECP ST
projects to be released through Spack.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
 2017-09-22 11:27:28 -06:00
sknigh
7b4d8d6d1e Version fixes for py-csvkit (#5393) 2017-09-22 10:06:15 -07:00
healther
6ff57bde42 Add package py-memory-profiler (#5413) 
* add package memory profiler

* fix FIXME
 2017-09-21 20:00:09 -06:00
Yifan Zhu
77f2221177 r-s4vectors: created new package (#5419) 
* r-s4vecors: created new package

* Update package.py

* edited according to flake8
 2017-09-21 19:57:02 -06:00
Mike Pozulp
2ad3a1bff7 Update pic/shared variants for hdf5, python, silo (#5423) 2017-09-21 18:14:31 -07:00
lingnanyuan
3817111454 r-mpm: new package. (#5416) 2017-09-21 13:36:51 -07:00
Howard Pritchard
699f34c33f OpenMPI: add 2.1.2 bug fix release (#5418) 2017-09-21 13:26:23 -07:00