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2016-12-07add ACLOCAL_PATH updates for packages that register m4 macros (#2518)Tom Scogland1-0/+2
2016-12-07Fixed spelling of variable (#2516)Oliver Breitwieser2-2/+2
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 Smith0-0/+0
these packages (#2443) Funded-by: IDEAS Project: IDEAS/xSDK Time: 1 hour
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
2016-12-05Remove CYAML tests from Spack now that the DB is JSON. (#2487)Todd Gamblin1-4/+2
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
2016-12-05Use JSON for the database instead of YAML. (#2189)Todd Gamblin8-90/+282
* Use JSON for the database instead of YAML. - JSON is much faster than YAML *and* can preserve ordered keys. - 170x+ faster than Python YAML when using unordered dicts - 55x faster than Python YAML (both using OrderedDicts) - 8x faster than C YAML (with OrderedDicts) - JSON is built into Python, unlike C YAML, so doesn't add a dependency. - Don't need human readability for the package database. - JSON requires no major changes to the code -- same object model as YAML. - add to_json, from_json methods to spec. * Add tests to ensure JSON and YAML don't need to be ordered in DB. * Write index.json first time it's not found instead of requiring reindex. * flake8 bug.
2016-12-05Allow spack create to handle packages with period in name (#2351)Adam J. Stewart3-10/+13
* Allow spack create to handle packages with period in name * Update tests to handle new package name detection scheme
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
2016-12-05travis: sphinx does not support python 2.6 anymore (#2485)Massimiliano Culpo1-0/+3
2016-12-04Bugfix: restore `__contains__` method after ArchSpec refactor. (#2481)Todd Gamblin1-0/+3
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
2016-12-03Fixes to Handling Multiple Architectures (#2261)Joseph Ciurej13-272/+473
* Added some notes about how multiarch detection could be fixed. * Implemented a preliminary version of the "spack.spec.ArchSpec" class. * Updated the "spack.spec.Spec" class to use "ArchSpec" instead of "Arch". * Fixed a number of small bugs in the "spack.spec.ArchSpec" class. * Fixed the 'Concretizer.concretize_architecture' method so that it uses the new architecture specs. * Updated the package class to properly use arch specs. Removed a number of unused architecture functions. * Fixed up a number of bugs that were causing the regression tests to fail. Added a couple of additional regression tests related to architecture parsing/specification. Fixed a few bugs with setting reserved os/target values on "ArchSpec" objects. Removed a number of unnecessary functions in the "spack.architecture" and "spack.concretize" modules. * Fixed a few bugs with reading architecture information from specs. Updated the tests to use a uniform architecture to improve reliability. Fixed a few minor style issues. * Adapted the compiler component of Spack to use arch specs. * Implemented more test cases for the extended architecture spec features. Improved error detection for multiple arch components in a spec. * Fix for backwards compatibility with v0.8 and prior * Changed os to unknown for compatibility specs * Use `spack09` instead of `spackcompat` for the platform of old specs.
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.
2016-12-01Does nothing if no prexisting config.guess is found. (#2446)Matt Belhorn1-1/+3
* Does nothing if no prexisting config.guess is found. * Update name for RHEL OS.
2016-12-01Update tutorial_sc16_packaging.rst (#2450)TomasPuverle1-1/+1
Fixed a typo.
2016-12-01Update workflows.rst (#2451)TomasPuverle1-1/+1
Fixed a typo.
2016-12-01More informative help messages for spack config. (#2453)Sergey Kosukhin1-2/+10
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.
2016-11-29Allow shell support to work when set -u is set (#2418)Adam J. Stewart1-1/+1
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'.
2016-11-29CDash fixes (#2438)hegner1-4/+4
use short spec instead of spec as CDash has a limitation in name length mark all problems as 'FAILED' as CDash does not understand "ERRORED" status
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
2016-11-29add headers neede for CDASH to junit output (#2433)hegner1-2/+6
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
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