Commit graph

6109 commits

Author SHA1 Message Date
Luca Heltai
c25759e1c8 Added gsl dependency to pnfft (#8255) 2018-05-24 16:24:47 -05:00
Geoff Womeldorff
fdb2d6f493 kokkos: update kokkos spackage to add current host/gpu architectures. (#8226)
* kokkos: update kokkos spackage to add current host/gpu architectures.

* kokkos: simplify host/gpu architecture selection and make intent of arg population logic more clear.

* kokkos: mollify flake8.

* Make strings and logic more pythonic. Add error for GPU arch without CUDA.

* kokkos: simplify conflicts behaviour. make args population more pythonic.

* kokkos: move gpu values to list for use in variant and conflicts checking.

* kokkos: How fortunate the man with None.

* kokkos: fix gpu_arch conflict loop error. add conflict to guard against +cuda and 2.5.00:develop versions, until kokkos issue #1296 is resolved.

* kokkos: mollify flake8.

* kokkos: add descriptive message to version conflict with +cuda.
2018-05-24 10:53:58 -05:00
Matthias Diener
4c4e2866d8 Charm++: Add possibility to build git version (#8260) 2018-05-24 10:48:37 -05:00
Sajid Ali
5fff4da5b7 Add msgpack-c 3.0.1 (#8264)
* 	new file:   cpp-3.0.1.tar.gz
	modified:   package.py

* 	deleted:    cpp-3.0.1.tar.gz

* remove whitespace
2018-05-24 10:47:31 -05:00
Levi Baber
fdf889264e trf: make executable (#8265) 2018-05-24 10:47:17 -05:00
Chris Hadjigeorgiou
db4062b01f openfoam-org: add v2.4.0 (#7850)
Add 2.4.0 changes
2018-05-24 08:44:41 -07:00
jkelling
fa1153d116 Fix MD5 hash for opencv 3.2.0 and 3.1.0 release (#8241) 2018-05-24 08:59:11 -05:00
George Hartzell
80e4c7da0e Add info for datamash@1.3 (#8261) 2018-05-23 18:40:14 -05:00
Adam J. Stewart
9b9980256f
Add kealib 1.4.7 (#8235)
* Add kealib 1.4.7

* Fix out-of-source builds

* Remove username from kealib hg clone
2018-05-23 18:36:12 -05:00
Adam J. Stewart
8f3d717a30
Add PROJ 5.0.1 (#8233)
* Add PROJ 5.0.1

* proj-datumgrid resource must be placed in nad directory
2018-05-23 13:29:08 -05:00
Massimiliano Culpo
0ea8c4f3b2 mvapich2: added a proper libs attribute (#8253) 2018-05-23 13:28:21 -05:00
Adam J. Stewart
13a1575452
Add pkgconf 1.4.2 (#8256) 2018-05-23 13:27:39 -05:00
Adam J. Stewart
f57ce38c41
Add ncurses 6.1 (#8257) 2018-05-23 13:27:22 -05:00
Edward Kim
011d1245fb charm: Update install script (#7291)
* charm: Update install script

* Addressed PR comments

* Removed destination and suffix variants

* Added back parallel support
2018-05-23 13:26:59 -05:00
Massimiliano Culpo
9fee111741 gromacs: added version 2018.1 (#8251) 2018-05-23 10:13:09 -05:00
Massimiliano Culpo
251019c5e4 cgal: added version 4.12 (#8252) 2018-05-23 10:11:03 -05:00
Tim Law
60df206648 Update BookLeaf_Cpp and Typhon packages. (#8249) 2018-05-23 07:28:15 -05:00
Leonhard Reichenbach
ace283d594 Add latest versions of bazel (#8250) 2018-05-23 07:27:45 -05:00
Sinan
bc73e85af8 Package/mirdeep/fix for new url take2 (#8247)
* rename: mirdeep -> mirdeep2

* fixes for new url
2018-05-23 07:25:42 -05:00
Leonhard Reichenbach
3712ac1f66 Create new package: memkind (#8242)
* Create new package: memkind

* some style changes

* fix type of numactl dependency

* fix flake8 errors

* use patch() instead of a custom build phase
2018-05-22 13:37:03 -05:00
Adam J. Stewart
4d3ed1ff13
Add py-docopt package (#8236) 2018-05-22 10:49:12 -05:00
Massimiliano Culpo
0106c6cab7
subread: added version 1.6.2 (#8239) 2018-05-22 14:16:06 +02:00
Axel Huebl
cd72312940 CUDA 9.2 (#8238)
Add the latest CUDA release, v9.2 and updated CUDA Compatibility Matrix
2018-05-22 12:45:47 +02:00
Tim Stavenger
b61175aeba Update GlobalArrays package to new releases (#7840)
* update globalarrays package to current releases

* rename class to Globalarrays to match package folder

* rename bytes to int64, minor cleanup of descriptions

* int64 False by default

* remove reference to external as we aren't supplying paths, and use args.append()

* correcting args.append syntax

* add conflicts
2018-05-21 20:06:29 -05:00
Elizabeth Fischer
68e7fd053e gdbm: Get working on CentOS5 and Other Older Systems (#8134)
* Fix #7691

* flake8

* code review
2018-05-21 16:24:38 -05:00
Elizabeth Fischer
90d36016ef netcdf-cxx4: Update to use CPPFLAGS (#8148)
* Fix bug; don't know why this ever worked in the first place.

* Add fix to netcdf-fortran too; flake8

* Simplify configure_args()

* netcdf-fortran: simplify that too
2018-05-21 16:23:35 -05:00
lingnanyuan
646771300d Create new package: fastgbs and its dependency platypus. (#8174)
* pushing partially done recipe for fast-gbs and platypus

* modify platypus

* change header

* fast-gbs: change dependency type.

* modify dependency type.

* modify dependency type.

* fast-gbs: Change dependency type to run.
2018-05-21 16:13:05 -05:00
peetsv
2cfde03a60 r-cghflasso v0 2 1 - new package (#8177)
* py-pyfaidx: adding new package

* updating the url

* r-cghflasso v0.2-1 new package

* correcting copy/paste error

* adding list_url
2018-05-21 16:12:35 -05:00
Jim Galarowicz
d7aaf4e193 Add urls into cbtf* and openspeedshop* package files and update the release versions for the Krell products (#8188) 2018-05-21 16:03:31 -05:00
Dan FitzGerald
8564be5479 Rename Tpetra C wrappers for *gemm Fortran functions in Trilinos 12.12.1 (#8228)
* Updated trilinos to compile/install with xl_r

* Undo PGI patch added as part of Trilinos XL fix

* Remove PGI related changes in Trilinos XL fix
2018-05-21 16:00:10 -05:00
Adam J. Stewart
fba365dc6a
Add Python/Ruby bindings to GEOS package (#8218)
* Add python/ruby bindings to GEOS package

* Add comment on Python 3 support
2018-05-21 15:59:50 -05:00
Adam J. Stewart
ac2b0f3ac0
Add lcms 2.9 (#8219) 2018-05-21 15:59:11 -05:00
Adam J. Stewart
ed0f5e9b4c
Add missing dependencies to poppler package (#8220) 2018-05-21 15:58:51 -05:00
Adam J. Stewart
729c3f9168
Add bmake 20180512 (#8221)
* Add bmake 20180512

* Re-add manpage patch
2018-05-21 15:58:11 -05:00
Eric
6ec603860a py-testinfra: Add versions 1.12.0 and 1.13.0 (#8222) 2018-05-21 15:57:25 -05:00
mcneish1
15634c20fe Update the hash of libjpeg v9c. (#8230)
The maintainer redid the archive in March, removing a .directory file.
2018-05-21 15:53:55 -05:00
Adam J. Stewart
6bf9f66567
Add cryptopp 7.0.0 (#8224) 2018-05-21 11:52:25 -05:00
Massimiliano Culpo
e933ed2b50
Updated sbt to point to github. Added versions 1.1.4, 0.13.17. (#7951) 2018-05-21 16:58:23 +02:00
Adam J. Stewart
7e04b20f3e
Add PCRE2 10.31 (#8214) 2018-05-20 15:05:47 -05:00
Adam J. Stewart
7b5c76552a
Add PCRE 8.42 (#8213) 2018-05-20 15:05:29 -05:00
Adam J. Stewart
e0d7e8ebd2
Add sqlite 3.23.1 (#8212) 2018-05-20 15:05:11 -05:00
Adam J. Stewart
a5d2e59320
Add libxml2 2.9.8 (#8211) 2018-05-20 15:04:47 -05:00
Adam J. Stewart
478c99ce01
Add cURL 7.60.0 (#8210) 2018-05-20 15:04:28 -05:00
Adam J. Stewart
e0dad09ea2
Add Xerces-C++ 3.2.1 (#8208) 2018-05-20 15:04:06 -05:00
Adam J. Stewart
15d102acec
Add FYBA package (#8205) 2018-05-20 15:03:38 -05:00
Adam J. Stewart
04687598c9
Add libgeotiff package (#8203) 2018-05-20 15:02:49 -05:00
Adam J. Stewart
0a47db5088
Add xz 5.2.4 (#8202) 2018-05-20 15:01:33 -05:00
Adam J. Stewart
17e6260d4b
Add libtiff 4.0.9 (#8201) 2018-05-20 15:01:11 -05:00
peetsv
1ec0f37897 r-utf8 v1.1.3 - New package (#8206)
* py-pyfaidx: adding new package

* updating the url

* r-utf8 v1.1.3 - New package

* adding list_url
2018-05-19 16:23:03 -05:00
peetsv
f9c35b2f04 r-spatial v7.3.11 - New package (#8204)
* py-pyfaidx: adding new package

* updating the url

* r-spatial v7.3.11 - New package
2018-05-19 13:12:47 -05:00
peetsv
96aedae886 r-proc v1 12 1 - New package (#8191)
* py-pyfaidx: adding new package

* updating the url

* r-proc v1.12.1 new package

* adding list_url
2018-05-19 11:26:44 -05:00
健美猞猁
2f5c4be3bf sleef: a new library. (#8198) 2018-05-19 11:26:31 -05:00
George Hartzell
9f85ad84ef neovim: add info for v0.2.2 (#8189) 2018-05-18 20:29:32 -05:00
mcneish1
f2eb71ca20 Fix libjpeg library finding and opencv build with nonstandard library directories (#8160) (#8179)
* Use libs[0] and headers.directories[0] instead of hardcoded paths in opencv dependencies

* Fix library finding in libjpeg-turbo

* Use build_type=Debug instead of +debug to determine build_type
2018-05-18 15:30:25 -07:00
Elizabeth Fischer
780cc9d72d antlr: Turn off CSharp (#8157)
Spack doesn't have a CSharp package, so the only time ANTLR would
succeed is if a system-installed CSharp was available. This disables
CSharp support, which enables building on systems without
system-installed CSharp.
2018-05-18 10:39:30 -07:00
Jon Rood
5641c1923b Turning off parallel during make install for parallel-netcdf. (#8186) 2018-05-18 12:12:43 -05:00
sknigh
c4cc6cde30 Added vim 8.1 (#8185) 2018-05-18 12:07:05 -05:00
Eric
e5b81dd566 task: Add version 2.5.1 (#8184) 2018-05-18 10:28:19 -05:00
Elizabeth Fischer
6d2617b05d nco: Find NetCDF (#8159)
* nco: Find NetCDF properly

* flake8
2018-05-18 07:51:21 -05:00
Levi Baber
29b695ed40 trinity: add perl+threads dependency (#8143) 2018-05-18 07:47:33 -05:00
Elizabeth Fischer
99f678035a libexpat: Fix for older systems, move to GitHub (#8135)
* PR #4945 did not make this work on SuSE 11.  Adding the latest version of libexpat did.  Also update for Expat's move to GitHub.

* Update package.py

* Update package.py

Move to url_for_version()
2018-05-17 20:04:57 -05:00
Levi Baber
e7d5421baf trinity: fixing jdk dependency (#8140) 2018-05-17 20:03:36 -05:00
Levi Baber
c06174a081 perl: adding threads variant (#8142) 2018-05-17 20:02:07 -05:00
Daryl W. Grunau
457dadaac8 silo: support version 4.10.2-bsd (#8164) 2018-05-17 19:55:00 -05:00
Michael Kuhn
c80333704c Update scorep and friends to newest versions (#8171) 2018-05-17 19:52:01 -05:00
Serban Maerean
a020a41298 Changed netlib-lapack to fix an error in the CMake setup. (#8172)
* Changed netlib-lapack to fix an error in their CMake setup. Changed
netlib-lapack spackage file to add Fortran flags correctly for XL
compiler.

* Fixed line length -- forgot abt flake8...

* Fix the package version where the ibm patch applies.
2018-05-17 19:51:34 -05:00
peetsv
9f12b5aed6 R dismo 1 1 4 - new package (#8176)
* py-pyfaidx: adding new package

* updating the url

* r-dismo: new package
2018-05-17 19:50:19 -05:00
Matthias Diener
f3f9d04c32 cmake: update version (#8178) 2018-05-17 19:48:46 -05:00
Todd Gamblin
f202198777 Convert lazy singleton functions to Singleton object
- simplify the singleton pattern across the codebase
- reduce lines of code needed for crufty initialization
- reduce functions that need to mess with a global

- Singletons whose semantics changed:
  - spack.store.store() -> spack.store
  - spack.repo.path() -> spack.repo.path
  - spack.config.config() -> spack.config.config
  - spack.caches.fetch_cache() -> spack.caches.fetch_cache
  - spack.caches.misc_cache() -> spack.caches.misc_cache
2018-05-17 14:10:30 -07:00
Todd Gamblin
6f2cac9565 init: initialize spack.store lazily
- spack.store was previously initialized at the spack.store module level,
  but this means the store has to be initialized on every spack call.

- this moves the state in spack.store to a singleton so that the store is
  only initialized when needed.
2018-05-17 14:10:30 -07:00
Todd Gamblin
a4d276fbe4 init: factor paths out of spack/__init__.py and into spack.paths module 2018-05-17 14:10:30 -07:00
Denis Davydov
d579231967 flex: use 2.6.3. by default (#8154)
Fixes #8152

Flex 2.6.4 doesn't build with gcc@7:. This sets Flex 2.6.3 as the
preferred version. The flex package had a conflict directive for
this but originally the recorded conflict was specific to ubuntu;
this appears to be an issue on multiple operating systems so this
also updates the conflict to be more general and adds a comment
which links to the relevant issues.
2018-05-17 13:58:29 -07:00
lingnanyuan
a46f2b8e42 swap-assembler: Create new package. (#8144)
* swap-assembler: Create new package.

* swap-assembler: fix flake8 error.
2018-05-17 15:43:30 -05:00
Christoph Junghans
110511da92 pv: initial commit (#8147) 2018-05-17 15:40:54 -05:00
Levi Baber
0141581a66 r-rstan: new version and dependents (#8158)
* r-stanheaders: new version

* r-rstan: new version

* r-rcppeigen: new version

* r-rstan: requires newer version of r-rcppeigen
2018-05-17 15:26:38 -05:00
Serban Maerean
e24a56b8cb Add version 6.1. to ESSL spackage file. (#8170) 2018-05-17 15:04:28 -05:00
Jim Galarowicz
dfd168d557 cbtf-argonavis-gui: add openspeedshop-utils package to address qt conflicts (#8066)
Fixes #7946

Creates an openspeedshop-utils package that does not depend on qt3
and can be used to resolve the needs of cbtf-argonavis-gui.

Changes for creating a release versus develop build are also
included. There are package versions which are no longer relevant
(e.g. 1.3.0 for cbtf-argonavis-gui has been replaced with 1.3.0.0)
but these versions need to be kept to allow uninstalling them;
issue #8173 has been created to investigate this.
2018-05-17 12:04:33 -07:00
Adam J. Stewart
de7d13b0e8
Add dependencies for py-dask (#8120) 2018-05-16 22:54:33 -05:00
健美猞猁
b895386fd7 r-rcppcnpy: a new package. (#8139)
* r-rcppcnpy: a new package.

* Specify dependency versions.

* Update dependency.
2018-05-16 12:45:24 -05:00
Eric
218e32991d Add list_url to allow download of prior versions from cran archive (#8141) 2018-05-15 22:10:20 -05:00
David Böhme
e3035fb91a Add libunwind-1.2.1 (#8145) 2018-05-15 13:54:23 -07:00
Denis Davydov
e0dcd87af9 astyle: add 3.1 (#8137) 2018-05-15 09:43:27 -05:00
Serban Maerean
0598f70de2 patch petsc test cases for XL compiler (#8091)
- After spack install, these test cases are built in a seperate step, outside of spack, but they need to patched after staging so users don't have to do it in a seperate step.

- The test cases are installed under `<petsc install directory>/share/petsc/examples` and can be built and executed by invoking `gmake -f gmakefile.test` in that directory.
2018-05-14 23:53:05 -07:00
Robert Pavel
b956608631 Added Shim to Support hdf5+mpi in Spack Silo (#8130)
* Added Shim to Support hdf5+mpi in Spack Silo

Added compatibility for hdf5+mpi to silo spackage to support spackages
with dependency chains that include silo and hf5+mpi

* Fixed fixable flake8 issue with silo spackage

Fixed missing whitespace around operator

* Setting MPI Variant to Default to True

As per guidance changing variant to default to MPI builds
2018-05-14 20:29:03 -05:00
snehring
538d617d14 salmon: adding in version restriction for boost (#8129)
1.67 does not work with this
2018-05-14 18:48:28 -05:00
Cameron Smith
3a7fadd67e prenek missing X.h (#8121) 2018-05-14 18:19:46 -05:00
lingnanyuan
34a2d35e50 lordec: Create new package. (#8095)
* lordec: Create new package.

* lordec: Add homepage, change to MakefilePackage.

* Modify dependency type.
2018-05-14 16:56:49 -05:00
Eric
6cf1d25d14 r-fit-models: Create new package (#8122) 2018-05-14 16:50:54 -05:00
Eric
c5b1336b69 r-vipor: Create new package (#8128) 2018-05-14 16:38:59 -05:00
Brian Van Essen
281e22ed73 LBANN: add hydrogen as optional dependency (#8085)
Add Hydrogen package for fork of Elemental library. Update LBANN
to use either Hydrogen or Elemental.
2018-05-14 11:58:34 -07:00
Eric
e7a737621f r-shinydashboard: Create new package (#8116) 2018-05-14 13:00:18 -05:00
Eric
28982bd103 r-picante: Create new package (#8117)
* r-picante: Create new package

* Remove dependency already included in RPackage base class
2018-05-14 13:00:03 -05:00
Eric
f2cc7f769b r-squash: Create new package (#8118)
* r-squash: Create new package

* Remove dependency already included in RPackage base class

* remove extra file
2018-05-14 12:59:49 -05:00
Sajid Ali
a47ff73c6e Update py-llvmlite to reflect llvm@6 requirement for versions >0.23.0 (#8109)
* 	new file:   package.py

* corrected using pep8online.com

* Update package.py

* correct typo

* as requested

* 	modified:   package.py

* Update package.py
2018-05-14 11:26:01 -05:00
Levi Baber
b5d578a5e1 Aegean: new package (#8113)
* aegean: new package

* genometools: set dependent env for aegean
2018-05-14 11:10:19 -05:00
Christoph Junghans
1aef372fbf charliecloud: fix copyright (#8115) 2018-05-14 11:09:57 -05:00
Denis Davydov
42137d59ef dealii: another fix for quick tests only in 9.0 and thus hash (#8114) 2018-05-14 11:07:19 -05:00
健美猞猁
341132a87f A new pacakge: Kaiju. (#8111)
* A new package: kaiju.

* Replace ftp:// with https://.
2018-05-14 11:07:00 -05:00
Levi Baber
32662c4edb hisea: new package (#8112) 2018-05-14 09:46:54 -05:00
Sajid Ali
0dabe81a20 Add numexpr 3 (#8107)
* 	new file:   package.py

* corrected using pep8online.com

* Update package.py

* correct typo

* as requested
2018-05-14 09:46:14 -05:00