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2016-12-19NCO: Add latest version, update to AutotoolsPackage (#2629)Adam J. Stewart1-9/+11
2016-12-18Add gawk (GNU awk) (#2625)Todd Gamblin1-0/+45
* Add gawk, GNU awk. * flake8 fix.
2016-12-18Feature/add package for fastqc (#1573)George Hartzell2-0/+90
* Add package for fastqc This tool is a java mess. Their Way To Do It is to just copy the entire tree into it's final resting place, make the perl script at the top level executable and take it from there. Yuck. This package assumes that `set_executable` actually sets all the user bits. If that change doesn't go in, then something equivalent needs to be done. * Use chmod to make fastqc executable I haven't gotten any feedback on changing set-executable, so switch to using chmod (from the cuda package). * Flake8 cleanup * Install files neatly, don't just copy top level of dir Rather than blindly copying everything in the distribution, carefully put the necessary bits into reasonable places. Neatness counts, etc... This requires patching the `fastqc` perl script, so this commit adds a patch file. * Additional pep8 cleanup * Let dependency handle adding jdk to PATH * Flake8 cleanup * Ensure that java is on PATH I thought that the run dependency on the jdk would put java on my PATH, but it does not appear to work. For now, do it by hand.
2016-12-18Added customization for make targets in 'build' and 'install' phases for ↵Alfredo Adolfo Gimenez2-4/+16
AutotoolsPackage (#2464) * Customization for make targets in build and test phases for AutotoolsPackage * Updated Blitz++ to use customized make build and test targets * Removed flake8 error * Removed make test customization, added make install customization, need to figure out issues with multiple make targets * Changed build_targets and install_targets to normal attributes
2016-12-18py-markdown: Add new package for python-markdown. (#2611)Chris MacMackin1-0/+61
* py-markdown: Add new package for python-markdown. * py-markdown: Added restrictions on Python version. * py-markdown: Removed upper-limit on compatible Python versions. * py-markdown: Reinstated upper bound on Python version. Also fixed small formatting error.
2016-12-18gmsh: add 2.15.0 and switch to CMakePackage (#2620)Denis Davydov1-10/+7
2016-12-18tbb: add 2017.3 (#2619)Denis Davydov1-0/+3
2016-12-18cmake: add 3.7.1 (#2618)Denis Davydov1-0/+1
2016-12-17build fixes for openblas (#2601)Gregory Lee1-0/+5
* build fixes for openblas * avx2 in openblas nnot supported with older gcc * merge fix for openblas
2016-12-17dealii: fix config for Netcdf with lib64 (#2616)Denis Davydov1-2/+13
2016-12-16graphviz: fixed build error due to specifying ltdl lib but not include. (#2609)Chris MacMackin1-2/+2
* graphviz: fixed build error due to specifying ltdl lib but not include. * graphviz: Fixed dependencies on libtool and expat.
2016-12-16libmesh: added mpi variant (#2584)Andrey Prokopenko1-1/+15
2016-12-16init nfft 3.3.2 package file (#2612)Thierry1-0/+60
* init nfft 3.3.2 package file * shorten comment line
2016-12-16py-beautifulsoup4: Added version 4.5.1 (#2610)Chris MacMackin1-0/+3
2016-12-16Updating Trilinos with superlu variant and fixing git branch version ↵Jon Rood1-1/+25
options. (#2604)
2016-12-16[HACK] Make concretization great again! (#2590)Adam J. Stewart16-16/+16
* Always default to +mpi * Always default to ~X
2016-12-15openblas: derives from MakefilePackage (#2488)Massimiliano Culpo3-57/+71
* MakefilePackage: changed build_args and install_args for consistency with #2464 openblas: derives from MakefilePackage * MakefilePackage: changed default edit behavior
2016-12-15go: see #2567, temporary fix (#2588)Massimiliano Culpo1-2/+8
2016-12-15Add GNU patch to Spack. (#2598)Todd Gamblin1-0/+37
2016-12-14Fix target for compiler on CNL operating systems (#2580)Mario Melara2-2/+2
Changes any to a string to avoid <built-in function any> being incorrectly added to target in compilers.yaml.
2016-12-14Blacklist flex 2.6.2 by commenting out package version (#2571)Jean-Paul Pelteret1-2/+4
Fixes #2554
2016-12-14Make unzip quiet (#2593)Adam J. Stewart2-1/+2
2016-12-14Update texlive digest (#2591)George Hartzell1-1/+1
Texlive is *live*, they update the contents of their tarball on a whim. Here's the current one.
2016-12-13New package py-cdo (#2569)Kim Serradell1-0/+47
* Add python cdo support * Correct pypi url * Corrected a blanck space that was failing CI * Corrected url that was failing CI * Following @alalazo indications, Write this line wrapping it around 80 chars to pass Travis * Added cdo package depency
2016-12-13Change attribute to match ArchSpec refactor (#2579)Mario Melara1-1/+1
Fixes issue #2578
2016-12-13Merge pull request #2506 from skosukhin/pr_pythonGregory Lee1-29/+134
A couple of updates for python package.
2016-12-13Better cxx11/14/17 flags for GNU/Clang/Intel (#2539)Ben Morgan4-2/+67
* Better cxx11/14 flags for GNU/Clang/Intel - GCC 4.8 only supports -std=c++1y for C++14 - Use CMake's rules for AppleClang to set cxx11 and cxx14 flags based on Apple Xcode/LLVM version - Use CMake's rules for Intel to add support for cxx14 flags based on Intel version. * Add cxx17_flag property Implement property in compiler for c++17 as per those for c++11/14. Add concrete support for GNU/Clang: - Return -std=c++1z for GCC 5 and above per GCC documentation - Return -std=c++1z for Clang 3.5 and above per Clang documentation - Return -std=c++1z for Apple LLVM 6.1 and above per CMake's rules
2016-12-13Added support for xSDKTrilinos package (#2201)amklinv1-0/+100
* Added support for xSDKTrilinos package * Updated xsdktrilinos/package.py for PR review * Added trilinos version # reqs to xsdktrilinos * xsdktrilinos now uses CMakePackage * Cleaned up xsdktrilinos/package.py * Removed unused cxxflags from xsdktrilinos * Removed unused sys import from xsdktrilinos
2016-12-13Update `spack setup` and `spack graph` to be consistent with recent ↵Elizabeth Fischer2-2/+4
refactoring (#2317) * Update `spack setup` and `spack graph` to be consistent with c557e765 and 9347f869. Fixes #2316. * Added another "fix" necessary to make `spack setup` work. * Added another "fix" necessary to make `spack setup` work. (reverted from commit 7f0d3ecb38c97ec00491d7cd66b4266e3018b1ca)
2016-12-13likwid: remote root from INSTALL_CHOWN (#2564)Denis Davydov1-3/+3
2016-12-13slepc/petsc: fix python dependency (#2560)Denis Davydov2-3/+5
2016-12-13Add a test to ensure package names have the right case. (#2562)Todd Gamblin4-5/+109
2016-12-13Updated python: refactoring and warning messages.Sergey Kosukhin1-36/+57
2016-12-13Updated python: pass LDSHARED to dependants' setup scripts.Sergey Kosukhin1-0/+88
2016-12-13Updated python: account for lib64 when filtering compilers.Sergey Kosukhin1-20/+16
2016-12-13Updated python: reformat code.Sergey Kosukhin1-10/+10
2016-12-12Add missing bzip2 dependency to freetype (#2536)Adam J. Stewart3-25/+23
* Add freetype dependency on bzip2 * Switch package with an install method for the docs
2016-12-12Doxygen: Add new version (#2561)Jean-Paul Pelteret1-0/+1
2016-12-12Set parent process's input stream inside the build process. (#2535)Sergey Kosukhin1-0/+13
2016-12-12p4est: remove unneded lua dependency (#2559)Denis Davydov1-1/+0
2016-12-12Add documentation for repositories and namespaces. (#2474)Todd Gamblin8-17/+476
* Add documentation for repositories and namespaces. * Update and extend repository documentation per review. - Also add `-N` argument for `spack spec`
2016-12-11New package - r-xgboost (#2493)Javier1-0/+54
2016-12-11atlas: fix lapack stage path (#2371)Denis Davydov1-5/+6
* atlas: fix lapack stage path * atlas: add a few links to other package managers
2016-12-11rename: add new package (#2486)Denis Davydov1-0/+45
2016-12-11[docs] missin .. code-block:: console in Spack 101 (#2530)Stephen McDowell1-0/+2
The advanced [Uninstalling Packages](spack.readthedocs.io/en/latest/tutorial_sc16_spack_basics.html#uninstalling-packages) via hash has a couple missing `.. code-block:: console` directives ;) I have no idea what branch to direct this to though...
2016-12-11likwid: add todo (#2531)Denis Davydov1-1/+9
* likwid: add todo * liwkid: add a note on hwloc dependency
2016-12-11numdiff: fix dependency type on macOS (#2538)Denis Davydov1-8/+2
2016-12-11Updated cmor: corrected way to set constraints for the extendee. (#2543)Sergey Kosukhin1-1/+2
2016-12-11Update Adol-C package (#2556)Jean-Paul Pelteret2-2/+3
Rename developer version, add new version, and make patch version specific.
2016-12-10clang: do xcode mockup iff requested by a package (#2544)Denis Davydov5-5/+15
* 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
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