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2016-12-25Better tabulation for spack checksum (#2673)Adam J. Stewart1-1/+5
2016-12-25filter_system_path: additionally filter system prefixes (#2672)Denis Davydov2-2/+6
That's because in set_build_environment_variables() the funciton filter_system_paths() is actually applied to package prefixes, and not to prefix/lib or prefix/include.
2016-12-25Add 64 bit variant to dealii. (#2654)Bruno Turcksin1-8/+15
2016-12-25Add latest version of Python 2 (#2668)Adam J. Stewart1-1/+4
2016-12-25Update gcc to 6.3.0 (#2669)Michael Kuhn1-0/+1
2016-12-25Add argument to `spack spec` to show deptypes. (#2680)Todd Gamblin2-1/+20
- `-t` | `--types` argument now shows deptypes in `spack spec`
2016-12-25Update the texlive distro digest. (#2679)George Hartzell1-1/+1
sigh.
2016-12-25Remove usernames from paths in docs (#2675)Adam J. Stewart9-303/+303
* Remove usernames from paths in docs * Fix path export
2016-12-25go: fixed GOROOT_BOOTSTRAP without workarounds (#2671)Massimiliano Culpo2-9/+5
2016-12-25Modify github archive regex to support luaposix (#2677)Adam J. Stewart2-1/+6
2016-12-21Update cairo to 1.14.8, gtkplus to 2.24.31 and pango to 1.40.3 (#2642)Michael Kuhn3-8/+10
2016-12-21Bug fontconfig (#2652)Kim Serradell2-1/+4
* Added uuid: OSSP uuid is a ISO-C:1999 application programming interface * Fixed install error in cmor package * Added uuid: OSSP uuid is a ISO-C:1999 application programming interface * Fixed install error in cmor package * Modifiying fontconfig file to allow install in OpenSuse 13.2 * Adding pkg-config dependency to freetype and libxml2 * Removed first possible solution. With @adamjstewart selecting the one adding pkg-config to dependencies
2016-12-21Fix homepage for the package libspatialindex (#2656)Federico Padua1-1/+1
Small fix for the homepage of the package libspatialindex.
2016-12-20Revert #2292: use frontend compiler for build deps (#2549)scheibelp4-90/+24
The primary goal of #2292 was to use the frontend compiler to make build dependencies like cmake on HPC platforms. It turns out that while this works in some cases, it did not handle cases where a package was a link dependency of the root and of a build dependency (and could produce incorrect concretizations which would not build).
2016-12-19Update gdal to 2.1.2 (#2643)Michael Kuhn1-2/+3
2016-12-19Various improvements to H5hut (#2636)Adam J. Stewart1-33/+38
2016-12-19Support Yorick versions (#2640)Todd Gamblin2-0/+9
2016-12-19moab: changed trilinos dependency to zoltan, and added fortran variant (#2582)Andrey Prokopenko1-2/+6
Trilinos dependency is very heavy, the zoltan one is light. I'm not sure if there is a situation where one needs the former.
2016-12-19Update PnetCDF to AutotoolsPackage (#2637)Adam J. Stewart1-10/+10
2016-12-19Update digest for vim@8.0 tarball. (#2600)George Hartzell1-16/+5
* Update digest for vim@8.0 tarball. The digest appears to have changed. The new digest value matches the value in their [MD5SUMS](ftp://ftp.vim.org/pub/vim/unix/MD5SUMS) file. * Change ftp.vim.org -> github.com/vim/vim/archive Vim seems to do weekly releases, but the name of the tarball on ftp.vim.org doesn't change so we have to regularly play 'update the digest' (aka Internet whack-a-mole). This commit changes the url so that we are now downloading particular versions from the Vim project's github archive. I didn't walk back through of time to get all of the versions that used to be explicit. I grabbed the final `7.4` and the current `8.0` releases. If people need more we can add them.
2016-12-19Modify github regex to support NCO. (#2633)Todd Gamblin2-1/+10
2016-12-19GSL: Add latest version, update to AutotoolsPackage (#2630)Adam J. Stewart1-16/+10
2016-12-19Fixes for various hash issues (#2626)Todd Gamblin10-59/+84
* Better output for disambiguate_specs() * Fix wrong exception name. * Fix satsifies(): concrete specs require matching by hash. - Fixes uninstall by hash and other places where we need to match a specific spec. - Fix an error in provider_index (satisfies() call was backwards) - Fix an error in satisfies_dependencies(): checks were too shallow. * Fix default args in Spec.tree() * Move installed_dependents() to DB to avoid unknown package error. * Make `spack find` and `sapck.store.db.query()` faster for hashes. * Add a test to ensure satisfies() respects concrete Specs' hashes.
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