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2018-12-04PNETCDF: Update with current versions (#9982)Greg Sjaardema1-3/+6
* PNETCDF: Update with current versions Added latest versions. (1.10.0, 1.9.0, 1.8.1) * PNETCDF: Revert version change in url Reverted the change in the url variable version since not required.
2018-12-04NETCDF: Add new versions and update url (#9970)Greg Sjaardema1-8/+14
* NETCDF: Add new versions and update url Added the 4.6.2 version which was recently released. Changed the url to point to the official Unidata site and added option to retrieve master version from git. * NETCDF: checksum and version updates Reverted back to use of previous URL. The `https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz` location is newer, but spack does not seem to be able to access all of the versions at that location -- only goes back to 4.5.0. Since several installations are still providing 4.4.0, thought it best to go back to previous url. However, it looks like the naming convention has changed since 4.6.2, so need to provide explicit url for 4.6.2. Probably best to go to a `url_for_version()` scheme if that naming convention stays in place?
2018-12-04boost: 1.68 also needs `boost_1.67.0_pgi.patch` (#9980)Bert Wesarg1-1/+1
Its in upstream with the upcoming 1.69 release though.
2018-12-04Disallow bcl2fastq2 on OS X (#9966)George Hartzell1-0/+3
* 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
2018-12-04Expand dependency on qt to allow qt4 (#9964)Neil Flood1-1/+1
2018-12-04petsc: when petsc is built with fortran [default in spack] its best to use ↵Satish Balay1-1/+1
hdf5+fortran (#9986)
2018-12-04r-optparse: new package (#9967)Neil Flood2-0/+22
2018-12-04pgi: Add checksum for PGI 18.10 (#9985)Nick Forrington1-0/+1
2018-12-04cmake: add version 3.13.1 (#9983)Matthias Diener1-0/+1
2018-12-04abyss: new version (#9981)Levi Baber1-0/+1
2018-12-04Added missing libtool dependencies to libvterm and unibilium (#10007)sknigh2-0/+4
2018-12-03Download CMake sources from the Github releases (#10003)Robert Maynard1-8/+1
Now that CMake is providing CMake release artifacts on github, we should prefer those as they have better download speeds and uptime.
2018-12-03Phist 1.7.4 (#9996)jthies1-0/+13
* packages/phist: new version 1.7.4 with new variant 'host' to enable/disable host-specific optimizations.
2018-11-30Bump vtkm to version 1.3 and add new features (#9968)HAOCHENG LIU1-27/+83
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)
2018-11-30hpctoolkit: overhaul to use spack dependencies (#9946)Mark W. Krentel2-48/+67
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.
2018-11-28New versions for a few python modules (#9969)jwallior7-4/+11
* 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
2018-11-28Add PLASMA version 18.11.0 and Lua variant (#9689)Piotr Luszczek1-1/+19
* Add PLASMA 18.11.1 with optional Lua and test for headers
2018-11-28Add f18 package (#9183)Ondřej Čertík1-0/+23
* 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
2018-11-28glib: disable SELinux explicitly (#9956)Michael Kuhn1-0/+2
2018-11-27bcl2fastq2 package: recursively delete after copy (#9959)George Hartzell1-2/+2
Fixes #9944 73c978d replaced a move with a copy, which cased rmdir to fail (as it expects an empty directory). This switches to use `shutil.rmtree` instead.
2018-11-27Fixing problems with lammps dependencies voropp and latte (#9909)Jon Rood3-2/+13
* Fixing problems with lammps dependencies voropp and latte. * Always replacing CFLAGS in voropp and specifying voropp+pic dependency in lammps.
2018-11-27git: add version 2.19.2 (#9961)Matthias Diener1-1/+6
Also fixes instructions for new releases
2018-11-27Rename py-proj to py-pyproj, consistent with Spack's current naming ↵Neil Flood3-4/+4
conventions (#9962)
2018-11-27new package: add support for the tfel package (#9930)thelfer1-0/+96
2018-11-26py-pygobject: add missing pkgconfig dependency (#9955)Michael Kuhn1-1/+2
2018-11-26OpenMPI: Prefer Last 3.X (#9945)Axel Huebl1-1/+1
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.
2018-11-26GATK: Add version 4.0.11.0 (#9953)Eric1-0/+1
2018-11-26minced: Add version 0.1.6 (#9951)Eric1-0/+1
2018-11-26hdf5: add version 1.8.21 (#9952)Matthias Diener1-0/+2
2018-11-26go: add 1.11.2 (#9948)Michael Kuhn1-0/+1
2018-11-26metabat: Add version 2.11.2 (#9950)Eric1-0/+1
2018-11-26Feature/gatk (#9872)Miles Perry1-6/+4
* added 3.8-1 version * fixed flake8 stuff
2018-11-26Uncomment dependencies previously disallowed by concretizer (#9942)Adam J. Stewart14-63/+22
2018-11-24Package/py scikit learn (#9843)Sinan1-3/+8
* add v0.20 specific dependency versions, also add cython and py-test as dependencies * make flake8 happy * make cython a build-only dependency
2018-11-24py-pygresql: new package (#9922)Neil Flood1-0/+19
* py-pygresql: new package * Added dependency on py-setuptools, as the build will use it if present
2018-11-24py-psycopg2: new package (#9926)Neil Flood1-0/+18
* py-psycopg2: new package * Added dependency on py-setuptools, as the build will use it if present
2018-11-24p4est: fix a typo (#9932)Denis Davydov1-1/+1
2018-11-24mc: add version 4.8.21 (#9943)Matthias Diener1-0/+1
2018-11-24intel-parallel-studio: add missing updates to 2019.1 (#9941)Matthias Diener2-0/+3
2018-11-24py-geopandas: New package. (#9919)Neil Flood5-0/+116
* 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
2018-11-24cmake: add version 3.13.0 (#9940)Matthias Diener1-0/+1
2018-11-24r-geor: new package, and a couple of its dependencies (#9920)Neil Flood4-0/+85
* 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.
2018-11-23new version 18.1 for py-pip (#9938)Andreas Baumbach1-0/+1
Change-Id: Ie462e802049dd6150767dc555fb5708999e081ec
2018-11-23r-compositions: new package, including its dependencies (#9921)Neil Flood3-0/+61
* 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
2018-11-22libspatialite: new package (#9923)Neil Flood2-0/+37
2018-11-22munge: update versions and url format to reflect switch to .xz format… (#9916)Nicholas Labello1-2/+3
* munge: update versions and url format to reflect switch to .xz format in recent releases * package:munge remove unneeded version-specific urls
2018-11-22minced: add version 0.3.2 and fix install paths (#9918)Eric1-2/+4
2018-11-22qca: new package (#9924)Neil Flood1-0/+25
2018-11-22qjson: new package (#9925)Neil Flood1-0/+18
2018-11-22p4est: apply patches to 2.0 only (#9928)Denis Davydov1-2/+4
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