Matthias Wolf
e3aa36f4cb
fix: adapt junit template to escape std{out,err} ( #9935 )
2018-12-04 14:05:45 +01:00
George Hartzell
0c3f220fb1
Disallow bcl2fastq2 on OS X ( #9966 )
...
* Disallow bcl2fastq2 on OS X
[Illumina's computing requirements][reqs] claim support for RHEL/CentOS and
go on to say:
> May be possible to install and run on other 64-bit Linux distributions or Unix variants.
The sufficient issue is its reliance of malloc.h. There may be more.
[reqs]: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/computing-requirements.html
* Add an informative msg for the user
2018-12-04 13:44:15 +01:00
Neil Flood
e3d204cb8f
Expand dependency on qt to allow qt4 ( #9964 )
2018-12-04 13:37:37 +01:00
Satish Balay
808c2ea5ce
petsc: when petsc is built with fortran [default in spack] its best to use hdf5+fortran ( #9986 )
2018-12-04 13:32:30 +01:00
Neil Flood
47b7016ea7
r-optparse: new package ( #9967 )
2018-12-04 13:20:08 +01:00
Nick Forrington
9551b34cb5
pgi: Add checksum for PGI 18.10 ( #9985 )
2018-12-04 13:12:20 +01:00
Matthias Diener
dfb02fd078
cmake: add version 3.13.1 ( #9983 )
2018-12-04 13:09:49 +01:00
Levi Baber
27e8fcb945
abyss: new version ( #9981 )
2018-12-04 13:02:36 +01:00
sknigh
a9695bac50
Added missing libtool dependencies to libvterm and unibilium ( #10007 )
2018-12-04 13:01:37 +01:00
Robert Maynard
0d033a042c
Download CMake sources from the Github releases ( #10003 )
...
Now that CMake is providing CMake release artifacts on github,
we should prefer those as they have better download speeds and
uptime.
2018-12-03 12:35:51 -06:00
jthies
3a2045b7c0
Phist 1.7.4 ( #9996 )
...
* packages/phist: new version 1.7.4 with new variant 'host' to enable/disable host-specific optimizations.
2018-12-03 09:40:51 -06:00
HAOCHENG LIU
66a62d82c4
Bump vtkm to version 1.3 and add new features ( #9968 )
...
This commit allows users to enable openmp, rendering, logging and mpi
in vtkm. Meanwhile, it adds support for cuda architecture selection.
[VTK-m 1.3 Release notes](https://gitlab.kitware.com/vtk/vtk-m/tags/v1.3.0 )
2018-11-30 19:48:22 -08:00
Mark W. Krentel
cc5446f25c
hpctoolkit: overhaul to use spack dependencies ( #9946 )
...
Overhaul hpctoolkit to AutotoolsPackage and to build its dependencies
directly from spack instead of using hpctoolkit-externals.
Remove hpctoolkit-externals since it's no longer needed.
2018-11-30 18:11:12 -08:00
jwallior
930debcf35
New versions for a few python modules ( #9969 )
...
* py-jupyter-console: Add version 5.2.0
* py-jupyter-core: add version 4.4.0
* py-lxml: add version 4.2.5
* py-zmq: add version 17.1.2
* py-terminado: add version 0.8.1
* py-pexpect: add version 4.6.0
* py-pytables: add version 3.4.4
2018-11-28 21:44:15 -06:00
Piotr Luszczek
8375b5b571
Add PLASMA version 18.11.0 and Lua variant ( #9689 )
...
* Add PLASMA 18.11.1 with optional Lua and test for headers
2018-11-28 16:59:05 -06:00
Ondřej Čertík
62f1cf3678
Add f18 package ( #9183 )
...
* Add f18 package
* Fix flake8 errors
* Install the f18 binary into prefix.bin by hand
* Add spack-build into the path
* Fix the license header
2018-11-28 14:13:30 -06:00
Massimiliano Culpo
e998a399da
Injected flags have a consistent order ( #9960 )
...
Fixes #9908
Spack was assembling flags in a manner that could in different
orderings for repeated concretizations of the same spec and config
2018-11-28 10:23:38 -08:00
Michael Kuhn
5cea4a75d7
glib: disable SELinux explicitly ( #9956 )
2018-11-28 10:06:17 +01:00
George Hartzell
e4e980ee97
bcl2fastq2 package: recursively delete after copy ( #9959 )
...
Fixes #9944
73c978d
2018-11-27 17:22:14 -08:00
Scott Wittenburg
33b112a60d
Expose option to save all dependencies when writing spec.yaml ( #9965 )
2018-11-27 17:13:39 -08:00
Jon Rood
4c3091b05e
Fixing problems with lammps dependencies voropp and latte ( #9909 )
...
* Fixing problems with lammps dependencies voropp and latte.
* Always replacing CFLAGS in voropp and specifying voropp+pic dependency in lammps.
2018-11-27 16:55:21 -07:00
Matthias Diener
2164181d0a
git: add version 2.19.2 ( #9961 )
...
Also fixes instructions for new releases
2018-11-27 16:32:22 -06:00
Neil Flood
8a78c9c6bc
Rename py-proj to py-pyproj, consistent with Spack's current naming conventions ( #9962 )
2018-11-27 16:31:30 -06:00
thelfer
2e04f3daab
new package: add support for the tfel package ( #9930 )
2018-11-27 07:16:55 +01:00
Michael Kuhn
16d3e44515
py-pygobject: add missing pkgconfig dependency ( #9955 )
2018-11-26 21:41:44 -06:00
Axel Huebl
b26c85301d
OpenMPI: Prefer Last 3.X ( #9945 )
...
The latest OpenMPI release, v4.0.0, does not build with many GCC
variants. Since this is our default, a lot of users get hit.
Let's wait for some point releases.
2018-11-26 16:46:04 -06:00
Eric
20a6dde10b
GATK: Add version 4.0.11.0 ( #9953 )
2018-11-26 14:54:05 -06:00
Eric
d9046e70c1
minced: Add version 0.1.6 ( #9951 )
2018-11-26 14:22:17 -06:00
Matthias Diener
bab3d7734a
hdf5: add version 1.8.21 ( #9952 )
2018-11-26 12:56:44 -06:00
Michael Kuhn
7df14134c1
go: add 1.11.2 ( #9948 )
2018-11-26 11:33:55 -06:00
Eric
5cd8233139
metabat: Add version 2.11.2 ( #9950 )
2018-11-26 11:32:14 -06:00
Miles Perry
28e93a7a79
Feature/gatk ( #9872 )
...
* added 3.8-1 version
* fixed flake8 stuff
2018-11-26 11:30:21 -06:00
Adam J. Stewart
06dcf72f14
Uncomment dependencies previously disallowed by concretizer ( #9942 )
2018-11-26 09:11:16 +01:00
Sinan
096922c39d
Package/py scikit learn ( #9843 )
...
* add v0.20 specific dependency versions, also add cython and py-test as dependencies
* make flake8 happy
* make cython a build-only dependency
2018-11-24 19:03:30 -06:00
Neil Flood
4c1733bff4
py-pygresql: new package ( #9922 )
...
* py-pygresql: new package
* Added dependency on py-setuptools, as the build will use it if present
2018-11-24 17:45:27 -06:00
Neil Flood
e3e01ab3d7
py-psycopg2: new package ( #9926 )
...
* py-psycopg2: new package
* Added dependency on py-setuptools, as the build will use it if present
2018-11-24 17:45:16 -06:00
Denis Davydov
058a772a52
p4est: fix a typo ( #9932 )
2018-11-24 17:45:04 -06:00
Matthias Diener
9d2ea84112
mc: add version 4.8.21 ( #9943 )
2018-11-24 17:42:46 -06:00
Matthias Diener
e86a28aff7
intel-parallel-studio: add missing updates to 2019.1 ( #9941 )
2018-11-24 15:44:57 -06:00
Neil Flood
9945a59c47
py-geopandas: New package. ( #9919 )
...
* py-geopandas: New package, including packages for its dependencies
* Trailing whitespace removed, etc
* One more trailing whitespace
* Removed some extraneous dependencies. No idea why I thought I needed them, but it now builds fine without them.
* Added a variant +plotting, to include the dependencies required for plotting, as these are large-ish if not being used.
* Added explicit dependency on py-matplotlib
2018-11-24 15:44:44 -06:00
Matthias Diener
25b9938ad1
cmake: add version 3.13.0 ( #9940 )
2018-11-24 14:23:10 -06:00
Neil Flood
a0fc573ff4
r-geor: new package, and a couple of its dependencies ( #9920 )
...
* r-geor: new package, and a couple of its dependencies
* Update to new copyright header
* Include the list_url for the R package archive dir
* Added explicit version ranges on dependencies, as per the relevant CRAN pages
* Correct dependency types in r-splancs.
2018-11-24 14:21:54 -06:00
Andreas Baumbach
862d1799fb
new version 18.1 for py-pip ( #9938 )
...
Change-Id: Ie462e802049dd6150767dc555fb5708999e081ec
2018-11-23 18:09:20 -06:00
Neil Flood
2e510413c3
r-compositions: new package, including its dependencies ( #9921 )
...
* r-compositions: new package, including its dependencies
* Include the list_url for the R package archive dir
* Added explicit version ranges on dependencies, as per the relevant CRAN pages
2018-11-23 18:06:57 -06:00
Neil Flood
3557b6e149
libspatialite: new package ( #9923 )
2018-11-22 13:54:52 -06:00
Nicholas Labello
13f2e68688
munge: update versions and url format to reflect switch to .xz format… ( #9916 )
...
* munge: update versions and url format to reflect switch to .xz format in recent releases
* package:munge remove unneeded version-specific urls
2018-11-22 13:13:40 -06:00
Eric
be92d46962
minced: add version 0.3.2 and fix install paths ( #9918 )
2018-11-22 13:13:06 -06:00
Neil Flood
c42ceb886c
qca: new package ( #9924 )
2018-11-22 12:45:42 -06:00
Neil Flood
b6e664846a
qjson: new package ( #9925 )
2018-11-22 12:45:17 -06:00
Denis Davydov
0f6f3ece95
p4est: apply patches to 2.0 only ( #9928 )
2018-11-22 12:40:22 -06:00
