Commit graph

8746 commits

Author SHA1 Message Date
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
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
Cameron Smith
e6d3ab8405 cray: add comment about module use in packages.yaml (#7751)
This advises users to prefer `modules:` entries in `packages.yaml` on Cray.
2018-04-13 11:53:26 -07:00
becker33
b9c8cdcbe3
Fix when_spec inheritance for extensions (#7746)
Popping the when spec from kwargs in the extends directive breaks
class inheritance. Inheriting classes do not find their when spec.

We now get the when spec from kwargs instead, leaving it to be found
by any downstream package classes.
2018-04-13 11:38:34 -07:00
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
Veselin Dobrev
7f46ec49e7 Specify default providers for the glu virtual package. (#7733) 2018-04-12 13:30:49 -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