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2016-12-10clang: do xcode mockup iff requested by a package (#2544)Denis Davydov1-0/+2
* clang: do xcode mockup iff requested by a package * add a note * add pkg to setup_custom_environment() and decide whether or not to use mockup XCode there based on the package
2016-12-10Eigen 3.3.1 is latest stable version. (#2551)Stephen McDowell1-0/+1
Main page states [3.3.1 is latest stable](http://eigen.tuxfamily.org/index.php?title=Main_Page).
2016-12-10Scotch 6.0.4 is available. (#2552)Stephen McDowell1-0/+1
Source project page states [6.0.4 is latest stable](http://scotch.gforge.inria.fr/)
2016-12-10Implementation of spack file for Pflotran (#2444)Barry Smith2-1/+50
Supports installing both a "known version" of PETSc/PFlotran that works and the develop/master branches of both packages Funded-by: IDEAS Project: IDEAS/xSDK Time: 4 hour
2016-12-09update flux dependencies and package (#2541)Tom Scogland8-40/+90
* update flux dependencies and package * refinements from @adamjstewart * fix flux document generation The docbook-xsl package has been added, and correctly configures catalog files to generate documentation correctly with asciidoc.
2016-12-09astyle: do not set user/group when installing on macOS (#2542)Denis Davydov1-0/+5
* astyle: do not set user/group when installing on macOS * astyle: add new version
2016-12-09petsc: explicitly disable X11 (#2533)Denis Davydov1-2/+3
otherwise petsc may pickup libX11 on login nodes during config/build, but libX11 may not be available on computation nodes.
2016-12-08Added packages: cmor and uuid. (#2527)Sergey Kosukhin2-0/+108
* Added package 'uuid'. * Added package 'cmor'. * Updated 'cmor' and 'uuid': docstring formatting.
2016-12-08Add support for parsing R-XML URL versions. (#2525)Todd Gamblin1-1/+2
* Add support for parsing R-XML URL versions. * Better url-parse debug output. - just print the debug stuff all the time. * fix R-XML versions.
2016-12-08Update emacs: current release, use our x11 bits (#2052)George Hartzell4-12/+21
* Update emacs: current release, use our x11 bits Add checksum for 25.1 release. Rework the X support: - use Spack's X11 bits - add ability to specify an X toolkit (gtk or athena, default is gtk). - change toolkit names to align with Emacs' configure usage. * PEP8 cleanups. * glib dependency should not be type=build I'd like to blame that on a typo, but it's a few too many characters for that to be viable. I'm not sure what I was thinking. * Pass X variant down: emacs->pango->cairo * X variants default to False, warn on bad toolkit Change the X variants for emacs, pango and cairo to default to False. Check that the toolkit is a valid choice and give a reasonable error if not. * Fix flake8 issue, reword warning text * gtkplus needs to use +X variant for pango to work In order for a useful variant of pango to be built into the spec I needed to make the dependency on gtkplus explicitly specify it's X variant. The X variant is the default, but that wasn't enough to make it happy. Since it's happiness is the most imporant thing in the world, this change! :)
2016-12-08Scotch fails to build with latest flex (#2523)Adam J. Stewart1-1/+1
2016-12-08dealii: remove dependencies which are not needed (#2522)Denis Davydov1-4/+0
2016-12-07Add version/digest for emacs 25.1 (#2511)George Hartzell1-0/+1
* Add version/digest for emacs 25.1 * Put newest version at top of list
2016-12-07yaml-cpp: add boost dependency (#2517)Andrey Prokopenko1-3/+4
yaml-cpp has a boost dependency, and according to [yaml-cpp page](https://github.com/jbeder/yaml-cpp): yaml-cpp 0.5.3 has been released! This is a bug fix release. It also will be the last release that uses Boost; futures releases will require C++11 instead.
2016-12-07Building lua-luafilesystem requires a newish-git (#2515)George Hartzell1-0/+1
See #2059 for background. I'm unable to install `lmod` because lua-luafilesystem fails. The luarocks install bits attempt to do a shallow clone of the luafilesystem sources and the default git on my CentOS 7 test box (`git version 1.8.3.1`) fails. This adds a build dependency that ensures that a relatively modern git is available.
2016-12-07Update texlive digest value (#2514)George Hartzell1-2/+9
* Update texlive digest value While the discussion in #2494 progresses, this changes fixes the digest values so that builds succeeed. * Add warning that texlive is not repeatably installable
2016-12-07netcdf: add checksum for 4.3.3.1 version (#2509)Andrey Prokopenko1-3/+4
2016-12-07cmake: added checksum for 3.1.0 version (#2508)Andrey Prokopenko1-1/+2
2016-12-06hypre, superlu-dist, trilinos - support using develop/master branches of ↵Barry Smith3-2/+24
these packages (#2443) Funded-by: IDEAS Project: IDEAS/xSDK Time: 1 hour
2016-12-06Fixed a few minor issues with the 'fontconfig' package install script. (#2491)Joseph Ciurej1-4/+4
2016-12-05hdf5: added 'pic' variant (#2373)Andrey Prokopenko1-0/+7
2016-12-05Add Java support to OpenMPI (#2285)Adam J. Stewart1-55/+93
* Update OpenMPI to the AutotoolsPackage * Add Java support to OpenMPI * Fix missing commas * Be more specific about what versions support what flags * Revert description for thread_multiple variant
2016-12-05py-rtree: Added package (#1548)Elizabeth Fischer2-0/+95
* py-rtree: Added package * py-rtree = RTree (spatial indexing) data structure for Python * libspatialindex = Underlying C library wrapped by py-rtree * Flake8 and Copyright issues. * Fix Python syntax error. * Fixed dependency type error. * Added new version, based on updates requested in upstream PR * 1. Change cmake to build dependency. 2. Updated to CMakePackage
2016-12-05ghostcript-fonts: fix install on macOS (#2482)Denis Davydov1-1/+7
2016-12-05xextproto: fix on macOS by not running parallel build (#2483)Denis Davydov1-0/+2
2016-12-03Update go to 1.7.4 and 1.6.4 to fix security issues (#2467)George Hartzell1-5/+20
* Update go to 1.7.4 and 1.6.4 to fix security issues The go team recently rolled out two releases to address security issues. Details available on the [go release site](https://golang.org/doc/devel/release.html). This commit updates our explicitly supported versions. It also includes a comment about two CentOS requirements (enable user_namespace and ensure that the static c library is installed) that are required for the pacakges to pass their tests. * Flake8 cleanup
2016-12-03zlib: added 'pic' variant (#2470)Andrey Prokopenko1-0/+12
It looks more complicated because zlib has custom configure which does not support CFLAGS option. So instead, we take it from environment.
2016-12-03Update git package to include 2.11.0 (#2471)George Hartzell1-0/+1
2016-12-02Fix download URL and dependencies for py-pypar (#2430)hegner1-3/+7
* fix download URL and dependencies for py-pypar * use url_for_version in py-pypar
2016-12-02foam-extend: modification to accept flex version >= 2.6 (#2452)Nicolas Richart1-6/+23
* Modification to accept flex version >= 2.6 + bug fix on paraview dependency * flake8 "corrections"
2016-12-02doxygen: Disable unnecessary graphviz dependency by default. (#2323)Elizabeth Fischer1-1/+1
2016-12-02Updating SuperLU package to use pic_flag instead of -fPIC, and removing ↵Jon Rood1-9/+4
specific version for default install method. (#2456)
2016-12-02Updating yaml-cpp from Package to CMakePackage. (#2457)Jon Rood1-9/+11
2016-12-02new intel parallel studio versions (#2459)Gregory Lee1-6/+17
2016-12-01cmake: update the requirements for --no-system-jsoncpp option (#2312)Andrey Prokopenko1-1/+1
The option appeared in CMake 3.2 (specifically, in 3.2.0-rc2, see https://cmake.org/pipermail/cmake-developers/2015-February/024552.html).
2016-12-01Make X11 font install dir the font search default (#2203)George Hartzell1-2/+7
* Make X11 font install dir the font search default We install the X11 fonts into `/share/fonts` beneath the font-util installation prefix, but that directory is not one of the places that the font subsystem searches. This commit makes the fontconfig package depend on the font-util package, and then it makes ```python spec['font-util'].prefix + "/share/fonts" ``` be the fontconfig default font location. Before this change, plots drawn by R have bounding boxes where font glyphs should be. After this change fonts appear as expected. * Enrich description string (trigger new CI run) Improve the docstring for the package. Also interested in the side effect of triggering another CI run to see if the recent flake8 fix lets this PR run clean. * Flake8 cleanups
2016-12-01Fix py-scientificpython and py-argcomplete dependencies (#2420)hegner2-0/+3
* add missing py-numpy dependency to scipy * add missing setuptools build dependency to py-argcomplete
2016-12-01Updated hdf5: new versions added. (#2442)Sergey Kosukhin1-0/+11
* Updated hdf5: new versions added. * Updated hdf5: url_for_version() accounts for per-version urls.
2016-12-01Update trilinos version to 12.10.1 (#2454)Bruno Turcksin1-1/+2
2016-12-01likwid: add new package (#2455)Denis Davydov1-0/+61
2016-12-01Merge pull request #2364 from davydden/ips_mklGregory Lee1-1/+1
intel-parallel-studio: fix location of MKL libs
2016-11-30Update R&friends to use our X11 libs (#2053)George Hartzell3-0/+17
* Update R&friends to use our X11 libs Add `depends_on()`'s for R, Cairo, and Tk so that they use the Spack X bits. * Conditionalize X stuff on variant Another step towards hooking up the X stuff. There's still discussion happening on the issue, but this is better than the 'everything must build with X' state that it was in.
2016-11-29New package - r-irkernel (#2434)Javier2-0/+102
* New package - r-irkernel * New package - r-pbdzmq, dependency of r-irkernel * Adding blank line expected by flake8 tests
2016-11-29Added the '+debug' and '+except' variants to the 'tetgen' package. (#2370)Joseph Ciurej2-5/+78
Fixed a bug that was causing memory errors after asserts in 'tetgen@1.5.0'.
2016-11-29New package - r-rbokeh (#2436)Javier1-0/+55
2016-11-29jemalloc: Update to 4.3.1 (#2435)Erik Schnetter1-0/+1
This corrects a severe problem (segfault) on macos Sierra.
2016-11-29add support for installing the development (master) version of PETSc (#2431)Barry Smith2-0/+47
Funded-by: IDEAS Project: IDEAS/xSDK Time: .3 hours x
2016-11-28Fix building latest version of flex (#2401)Adam J. Stewart7-57/+96
* Fix building latest version of flex * Don't need when clause * Remove perl deps, shebang too long
2016-11-28add missing zeromq dependency to r-rzmq (#2425)hegner1-0/+2
2016-11-28New package - r-pryr (#2424)Javier1-0/+46