Commit graph

9032 commits

Author SHA1 Message Date
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
Matthew Scott Krafczyk
1b38631781 Add -d option to diy to specify source path move -j to common args (#5963) 2018-04-18 17:26:14 -05:00
Elizabeth Fischer
d3c1463b0a Fix bug/oversight in formatting error message. (#7810) 2018-04-18 15:05:37 -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
Adam J. Stewart
ef37cdb380
Autocomplete spack providers (#7783) 2018-04-17 09:33:04 -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
George Hartzell
669b85e6bc Activation of activated package just msg's (#7752)
Activating a package that is already activated now sends a `tty.msg`
and returns.

```
-bash-4.2$ ~/spack/bin/spack activate aspell6-en
==> Package aspell6-en/lc4v24f is already activated.
```
2018-04-17 07:44:08 -05:00
Matteo Guglielmi
07ebcb7f6b r-biocgenerics: package update (#7778) 2018-04-17 07:43:26 -05:00