Commit graph

5898 commits

Author SHA1 Message Date
Levi Baber
14e0307f04 ucx: needs numactl and rdma-core (#7836) 2018-04-25 10:34:55 -05:00
Levi Baber
a7ecb0364a psm: new package (#7834)
* psm: new package

* psm: setting latest stable to preferred
2018-04-25 10:34:31 -05:00
Levi Baber
0b284b45db rdma-core: new package (#7835)
* rdma-core: new package

* rdma-core: change to platform conflict
2018-04-25 10:33:30 -05:00
Levi Baber
a21571e737 libnl: new package (#7833)
* libnl: new package

* libnl: change platform constraint to a conflict
2018-04-25 10:33:01 -05:00
Sajid Ali
24f15a5f4b Added checksums for newer versions of numpy (#7853)
*  Committer: sajid <sajid@xrmlite.phys.northwestern.edu>

	modified:   var/spack/repos/builtin/packages/py-numpy/package.py

* Corrected typo

* removing whitespace

* remove whitespace

* remove whitespace, if not will do this in vim
2018-04-25 10:30:25 -05:00
Eric
4fdd24effa py-testinfra: Create new package (#7883)
* py-testinfra: Create new package

* py-testinfra: flake8 fixes

* py-testinfra: fix pytest version dependency

* py-testinfra: fix py-importlib version dependency
2018-04-25 10:29:45 -05:00
Levi Baber
0d5dd96762 fabtests: new package (#7837)
* fabtests: new package

* fabtests: fix hashes for github archive behavior & add libfabric dep

* fabtests: both versions confirmed working

* fabtests: use developer provided archive
2018-04-25 10:29:29 -05:00
健美猫
48a3cc67fc Add a new package: gloo. (#7894)
* Add a new package: gloo.

* Remove dependencies.
2018-04-25 10:05:16 -05:00
健美猫
fca267468e Add a new package: cpuinfo. (#7895) 2018-04-25 10:04:45 -05:00
健美猫
7095d4f414 Add a new package: fp16. (#7896) 2018-04-25 07:30:07 -05:00
Daniel Topa
82ac1571c2 Openmpi update multithread (#7893)
--enable-mpi-thread-multiple option not viable in Open MPI 3.0+

Signed-off-by: Dan Topa <dantopa@lanl.gov>
2018-04-25 07:01:17 +02:00
Eric
5f04b0c538 new package: py-weblogo (#7886) 2018-04-24 19:31:37 -07:00
Denis Davydov
f7da156879 petsc and slepc: add 3.9.0; hypre: add 2.14 (needed by petsc) (#7877) 2018-04-24 07:10:46 -05:00
Eric
8e1a7eaafa ARAGORN: Create new package (#7875) 2018-04-23 16:51:42 -05:00
Eric
e3c708fafe prinseq-lite: Create new package (#7873)
* prinseq-lite: Create new package

* prinseq-lite: set variant description and add dependency type
2018-04-23 16:11:27 -05:00
Ross Miller
b5d9a44e17 7851 pmix aarch64 (#7852)
* Fix build issue with PMIx on aarch64

Work around a bug in PMIx that causes build issues on aarch64.  Bug was
fixed in PMIx 2.1.1, so the spack package checks both the architecture
and the PMIx version.  Workaround is to just not build the PMIx test and
example code.

* Minor code cleanups

Minor corrections to make 'spack flake8' happy.

* Add support for version 2.1.1
2018-04-23 14:09:52 -05:00
Mark Olesen
50fb9352f0 New colm, ragel packages (#7867)
- Ragel is a parser and finite state machine generator that can be
  used as an alternative means for solving parsing problems without
  Flex.
2018-04-23 10:50:58 -05:00
健美猫
b33f01c799 Add a new version 5.4.1.7 for mono. (#7866) 2018-04-23 07:31:29 -05:00
Dan Ibanez
130d0c8b2e omega-h: new package (#7861)
* omega-h: new package

* omega-h: fix multiple package.py issues

* omega-h: use tarball checksum to avoid warning

* omega-h: wrap lines for flake8
2018-04-22 17:26:52 -05:00
Sinan
af82f5529d new package: racon (bioinformatics) (#7726)
* new package: racon (bioinformatics)

* add cmake_arg method
2018-04-22 07:54:48 -05:00
健美猫
708fe9f676 Add a new pacakage: HiC-Pro. (#7858)
* HiC-Pro: a new package.

* Flake8.

* Update.

* Remove nektar.
2018-04-21 13:08:56 -05:00
健美猫
b91b4a6c4d A new pacakge: IMP. (#7859) 2018-04-21 13:08:44 -05:00
lingnanyuan
f939895b1b py-mg-rast-tools: Create new package and its dependencies. (#7816)
* r-matr: Create new package.

* shocklibs: Create new package.

* r-biom-utils: Create new package.

* r-mgraster: Create new package

* py-poster: Create new package.

* py-requests-toolbelt: Create new package.

* perl-libwww-perl: Create new package.

* py-mg-rast-tools: Create new package.

* mg-rast-tools: Fix version constraints for dependencies.

* Change dependency type of py-setuptools.
2018-04-21 10:28:44 -05:00
Levi Baber
3274f16780 py-pymol: new package (#7823)
* py-pymol: new package

* py-pymol: needs python+tk
2018-04-21 10:28:09 -05:00
healther
8cc24fa20b add variant htmlreport to package cppcheck (#7824)
Change-Id: I31766d3ceb4fa8852b9bdc82444e36514e760f4b
2018-04-21 10:26:37 -05:00
Denis Davydov
5794f432a9 gnuplot: add 5.2.2 (#7831) 2018-04-21 10:24:36 -05:00
Denis Davydov
2dfd61080b dealii: disable +slepc with ~petsc (#7832) 2018-04-21 10:22:10 -05:00
Eric
a808553fa1 DIAMOND: Add version 0.9.20 (#7847)
* DIAMOND: Add version 0.9.20

* DIAMOND: add version 0.9.21
2018-04-21 09:57:06 -05:00
Levi Baber
5ae960c476 jellyfish: fixing url for v2 package retrieval (#7849) 2018-04-21 09:56:38 -05:00
健美猫
c8e3c94c6f self has no attribute named satisfies. (#7826) 2018-04-19 12:43:12 -05:00
Axel Huebl
26e9b3b74d openPMD-api (#7765)
* openPMD-api

Add a new package for openPMD-api.

openPMD is a meta-data standard (markup, schema) for hierarchical,
scientific particle and mesh based data.

openPMD-api is a library wrapping the underlying backends (HDF5,
ADIOS, ...) into a single, object-aware API.

* Repository: https://github.com/openPMD/openPMD-api
* Project: https://github.com/openPMD http://www.openPMD.org

* mpi variant forwarding: fix concretization
2018-04-19 09:04:07 -05:00
Levi Baber
d65fbf4c68 libxml2: adding subdir to cpath for deps (#7819)
* libxml2: adding subdir to cpath for deps

* libxml2: no join_path

* libxml2: fix cpath for run_env

* libxml2: typo
2018-04-19 09:01:11 -05:00
Levi Baber
7219f4a2aa freetype: adding subdir to cpath for deps (#7818)
* freetype: adding subdir to cpath for deps

* freetype: no join_path

* freetype: fix cpath for run_env
2018-04-19 09:00:49 -05:00
Kelly (KT) Thompson
4869b7312a Suite-sparse: provide patch to fix builts with clang@6.0.0. (#7811)
+ I am unable to build suite-sparse@5.2.0 with clang@6.0.0.  The build fails
  with the error:

```
     2397    [ 99%] Linking C executable wildtype_demo
     2398    make[4]: Leaving directory
  `/tmp/kellyt/spack-stage/spack-stage-w0XYhK/SuiteSparse/GraphBLAS/build'
  >> 2399    libgraphblas.so.2.0.1: undefined reference to `__fpclassify'
  >> 2400    clang-6.0: error: linker command failed with exit code 1 (use -v to
  see invocation)
  >> 2401    make[4]: *** [wildtype_demo] Error 1
```

+ This error appears because libgraphblas.so requires `-lm`, but that link
  dependency is not explicitly listed in GraphBLAS\CMakeLists.txt.
+ A patch file is provided to add this dependency.  The patch is only applied
  when the compiler is `%clang`.
2018-04-19 08:59:55 -05:00
healther
6d1097f99b add variants and conflicts for curl (#7804)
* add variants and conflicts for curl

* darwinssl - Apple's SSL/TLS implementation
* libssh    - use libssh implementation
* add darwin conflict for libssh{,2}
* add linux conflict for darwinssl

* remove openssl when +darwinssl

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2018-04-19 07:23:16 -05:00
Levi Baber
4ed613d7e1 freeglut: new package (#7820) 2018-04-18 19:49:42 -05:00
Levi Baber
ecdb3065ed glew: adding gl dependency (#7817) 2018-04-18 17:58:45 -05:00
Jim Galarowicz
0fc51a9c3e Simple updates to the Krell Institute OpenSpeedShop and CBTF components build package files. (#7812) 2018-04-18 14:05:53 -05:00
Levi Baber
5d39e76353 xrandr: needs randrproto (#7814)
* xrandr: needs xrandrproto

* xrandr: fix typo
2018-04-18 14:02:04 -05:00
Axel Huebl
5f73c2759d ADIOS 1.13.1 & SZ 1.4.12.3 (#7808)
* ADIOS 1.13.1

ADIOS 1.13.1 fixes several issues with zero-sized block
reading and writing when compression transports are used.

* SZ 1.4.12.3

Add the lastest SZ release used in ADIOS1.
2018-04-18 10:52:13 -05:00
Matteo Guglielmi
247f24e015 bcl2fastq2: package update (#7794)
* bcl2fastq2: package update

* package/bcl2fastq2: homepage fix

* package/bcl2fastq2: glob fix

* package/bcl2fastq2: code clean up

* package/bcl2fastq2: code clean up #2
2018-04-18 10:11:44 -05:00
Loic Hausammann
87747b888f Add grackle 3.1 (#7805) 2018-04-18 07:23:09 -05:00
Matthias Diener
d950aeee09 cmake: update version (#7802) 2018-04-17 17:26:03 -05:00
Eric
1b32a4e3a5 DIAMOND: add zlib dependency (#7801) 2018-04-17 15:59:23 -05:00
Adam J. Stewart
5854acd233 Add latest version of cURL (#7800) 2018-04-17 14:33:08 -06:00
Eric
b84424e879 bismark: Create new package (#7795)
* bismark: Create new package

* bismark: fix dependency types
2018-04-17 14:45:10 -05:00
Yifan Zhu
b4bdf0db80 psmc: new package (#7773)
* psmc: new package

* psmc: changed version number

* psmc: overwrite build phase
2018-04-17 13:30:30 -05:00
Eric
8e58bf21cf perl-statistics-pca: Create new package (#7796)
* perl-statistics-pca: Create new package

* perl-statistics-pca: fix dependency types
2018-04-17 13:30:12 -05:00
Matteo Guglielmi
8afdf3d148 r-biomart: package update (#7787) 2018-04-17 12:55:36 -05:00
Matteo Guglielmi
65da62751f r-delayedarray: package update (#7788) 2018-04-17 12:55:20 -05:00
Eric
d49182cb7a DIAMOND: add versions 0.9.19, 0.8.38, 0.8.26 (#7789) 2018-04-17 12:55:08 -05:00
Matteo Guglielmi
abbd51cd21 r-summarizedexperiment: package update (#7790) 2018-04-17 12:54:56 -05:00
Matteo Guglielmi
02181c951a r-genomicalignments: package update (#7791) 2018-04-17 12:54:36 -05:00
Matteo Guglielmi
025e608fd5 r-bsgenome: package update (#7792) 2018-04-17 12:54:04 -05:00
Matteo Guglielmi
7171f31425 r-topgo: package update (#7793) 2018-04-17 12:53:37 -05:00
Matteo Guglielmi
c392bfc7d6 r-s4vectors: package update (#7779)
* r-s4vectors: package update

* r-s4vectors: dependencies fix
2018-04-17 10:04:37 -05:00
Matteo Guglielmi
5272ed5ad0 r-biobase: package update (#7785) 2018-04-17 10:04:24 -05:00
Matteo Guglielmi
8907161c93 Package/r-iranges (#7780)
* r-iranges: package update

* r-iranges: package update

* r-iranges: dependencies fix
2018-04-17 09:36:12 -05:00
Matteo Guglielmi
c2559bdef3 r-genomicranges: package update (#7782)
* r-genomicranges: package update

* r-genomicranges: dependencies fix
2018-04-17 09:33:24 -05:00
Matthias Maiterth
ed4d0c5a87 Package/geopm (#7560)
* geopm: Added initial files for package geopm
and py-natsort dependency

* geopm: Updated variants for hwloc and mpi defaults

* geopm: Cleaned up unwanted hyphenation in description.

* geopm: updates according to change request.

* geopm: Updated minor change requests.

Clarification for ruby-ronn dependency included as a TODO.
This requires changes in the current configure and build process
which will be changed in a future version.

* geopm: changed to AutotoolsPackage and fixed hwloc

The changes for hwloc required to add a specific version bc of a
conflicting version of openmpi's hwloc dependency being below
1.99. This works but updates to this package should check if this
restriction is still required. (Thus TODO added)

* geopm: Added link dependencies (thanks for pointing this out).

Also removed empty line below class definition.

* geopm: Fixed depends_on according to package guide.

Removed wrong type 'run' and removed types for numactl, mpi and hwloc
to use default build & link type.

* geopm: Fixed and updated +doc dependencies

new pacakge ruby-ronn (package specified as in ruby-narray package)
Updated second +doc dependency doxygen.

* geopm: Changed args for Autotools specific feature.

Added enable_or_disable and with_or_without instead of if cascade.
Added overhead variant.
Also added missing dependency (default: build&link) for json-c).
2018-04-17 07:51:56 -05:00
Geoffrey Oxberry
40f0305bfa glvis@3.3: new package (#7166)
* glvis@3.3: new package

* mesa-glu: now provides 'glu' (GL Utility library)

* openglu: add package, provides glu

* [GLVis] Use MakefilePackage as base. Add 'develop' version.

Small tweaks in the makefile arguments.

* [GLVis] Locate the X11, GL and GLU libraries within their respective
prefixes. Set the C compiler in the makefile arguments.

* [GLVis] Fix a bug: the same variable was used for two different things.

* [libx11] Add the libs property

* [OpenGL] Add the libs property

* [OpenGLU] Add the libs property

* [GLVis] Use the libs properties of libx11, opengl, and openglu
2018-04-17 07:48:48 -05:00
Matteo Guglielmi
07ebcb7f6b r-biocgenerics: package update (#7778) 2018-04-17 07:43:26 -05:00
Matteo Guglielmi
f4cc57261b r-genomeinfodb: package update (#7781) 2018-04-17 07:43:11 -05:00
Matteo Guglielmi
1c8df39024 r-htmltable: package update (#7767)
* r-htmltable: package update

* r-htmltable: dependency fix

* r-htmltable: dependency fix #2

* r-htmltable: dependency fix #3
2018-04-17 07:26:37 -05:00
Christoph Junghans
b6d3feba20
ospac: fix compiler usage and install (#7776) 2018-04-16 15:56:37 -06:00
Yifan Zhu
e94808a560 miniasm: new package (#7772) 2018-04-16 16:06:09 -05:00
Yifan Zhu
625ead40e3 fermikit: new package (#7775) 2018-04-16 15:54:05 -05:00
Matteo Guglielmi
385a209ff9 r-limma: package update (#7763)
* r-limma: package update

* r-limma: dependency fix
2018-04-16 11:49:40 -05:00
Michael F. Herbst
61b3e60f1f Add libcint version 3.0.11 (#7764) 2018-04-16 11:49:13 -05:00
Matteo Guglielmi
63d8f87f54 r-hmisc: package update (#7766) 2018-04-16 10:16:00 -05:00
Matteo Guglielmi
be934c5781 r-data-table: package update (#7768) 2018-04-16 10:14:20 -05:00
Matteo Guglielmi
3ae6dd9f64 r-matrix: package update (#7769) 2018-04-16 10:14:00 -05:00
Matteo Guglielmi
33f2200bf7 r-deseq2: package update (#7770) 2018-04-16 10:13:45 -05:00
healther
d0c388ca68 add version 2.0.9 to py-slurm-pipeline (#7771)
Change-Id: I6b597076b0740d65b8aeaebf95f459745b1b1503
2018-04-16 10:13:06 -05:00
Christoph Junghans
826c1f88a3
votca-moo: removal (#7762)
votca-moo is now part of votca-ctp (see votca/ctp#93)
2018-04-14 16:18:11 -06:00
Christoph Junghans
dae4653920 eospac: initial commit (#7761)
* eospac: initial commit

* eospac: add stable version
2018-04-14 14:14:38 -05:00
Eric
c8f78676eb perl-moose: Add versions 2.2007,2.2009,2.2010 (#7758) 2018-04-13 19:08:13 -05:00
Eric
1d0ecce49f perl-devel-overloadinfo: Add version 0.005 (#7754) 2018-04-13 16:58:50 -05:00
Eric
b6a130703d prank: Add version 170427 (#7755) 2018-04-13 16:58:39 -05:00
Eric
d602d04d46 tcl: Add version 8.6.8 (#7756) 2018-04-13 16:58:25 -05:00
Eric
eaaf1666ba tk: Add version 8.6.8 (#7757) 2018-04-13 16:58:13 -05:00
Massimiliano Culpo
94fbd7b60d
flux: changed default value for doc variant to False (#7749)
fixes #2095
2018-04-13 15:58:58 +02:00
Raghu Raja
ef253f9db4 libfabric: added v1.6.0 and v1.5.3 (#7742) 2018-04-13 09:09:54 +02:00
Adam J. Stewart
b9b19e1660 Fix www.example.com homepages (#7744) 2018-04-13 07:08:10 +02:00
Eric
21914d36be py-illumina-utils: Create new package (#7745)
* py-illumina-utils: Create new package

* fix dependency types
2018-04-12 22:45:21 -05:00
Eric
0091fda57b perl-contextual-return: Create new package (#7741)
* perl-contextual-return: Create new package

* perl-contextual-return: Fix homepage url
2018-04-12 15:56:07 -05:00
Yifan Zhu
7d8e6b2eda New package r-tmixclust (#7658)
* r-tmixclust: new package

* r-cluster: hash changed

* r-cluster: removed 2.0.6 and added the latest 2.0.7-1
2018-04-12 14:51:51 -05:00
Howard Pritchard
f5e4befcac UCX: update for release 1.3.0 (#7740)
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-04-12 14:51:25 -05:00
Eric
11cbee6e92 perl-perlio-utf8-strict: Create new package (#7738) 2018-04-12 14:02:37 -05:00
Yifan Zhu
fde1e0ecb8 supernova: new package (#7719)
* runing a test

* supernova: new package

* removed with working_dir line
2018-04-12 13:31:18 -05:00
Eric
89b5403b79 perl-text-simpletable: Create new package (#7739) 2018-04-12 13:29:51 -05:00
Yifan Zhu
8a4268837e New package r-spem (#7657)
* r-truncnorm: new package added

* r-solnp: new package added

* r-spem: new package added

* r-truncnorm: removed dependency r-testthat
2018-04-12 12:55:10 -05:00
Eric
61875784df perl-math-matrixreal: Create new package (#7737) 2018-04-12 12:53:53 -05:00
healther
bc379ab919 fix dependencies for matplotlib@2.2.2 (#7735) 2018-04-12 12:53:30 -05:00
Eric
41867cf007 perl-want: Create new package (#7734) 2018-04-12 12:24:28 -05:00
Geoffrey Oxberry
bbdf586d14 glu: new virtual package; openglu: new package (#7162)
* mesa-glu: now provides 'glu' (GL Utility library)

* openglu: add package, provides glu

* openglu: add custom fetcher, remove nonsense url

Change openglu package to look like the opengl package in GitHub PR

* [OpenGLU] Fix a typo
2018-04-12 07:16:16 -07:00
Geoffrey Oxberry
0e4e7d05e4 opengl: make error throw on install, not fetch (#7063)
* opengl: make error throw on install, not fetch

* opengl: add configuration advice for darwin

* opengl: add more versions of GL/OpenGL

* opengl: improve documentation in comments

* [OpenGL] Fix formatting
2018-04-12 07:14:38 -07:00
healther
3608c4d3b5 add package py-gdbgui (#7715)
* add package py-gdbgui

Change-Id: I553e1e4c4f6385348190817199e05b25522b57b4

* fix alignment

* add setuptool runtimedependency

* add gdb run dependency
2018-04-11 21:30:23 -05:00
healther
3b44a2ff40 Add package py-slurm-pipeline (#7681)
* add package py-slurm-pipeline

Change-Id: Iade405a7e96f04e476cea76e460cac2ebdf21f95

* add missing py-six dependency

Change-Id: I382fa4139880c1a61af3f314c74ed6e7c2e88c5b

* Update package.py

* Update package.py

* Update package.py

* fix flake8
2018-04-11 14:25:08 -05:00
Simon Flood
ed5f68211e Add ANTs package (#7717)
* Add ants package

Add a package for ANTs (version 2.2.0)

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2018-04-11 14:22:23 -05:00