Commit graph

8767 commits

Author SHA1 Message Date
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
Matteo Guglielmi
f4cc57261b r-genomeinfodb: package update (#7781) 2018-04-17 07:43:11 -05:00
Massimiliano Culpo
4bf7ce7d99 Better error message for spack providers (#7748)
* Better error message for spack providers

fixes #1355

`spack providers` now outputs a sensible error message if non-virtual
specs are provided as arguments:
```
$ spack providers mpi zlib petsc
==> Error: non-virtual specs cannot be part of the query [zlib, petsc]
```

Formatting of the output changed slightly.

* Calling 'spack providers' without arguments print the virtual pkg list

Also, the error message in case of a wrong parameter has been improved
to show the list of valid packages.

* Avoid printing headers if stdout is not a tty

* The provider list is formatted with colify if not in a tty

* Added a test to check the list of providers returned from the command
2018-04-17 07:30:32 -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