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2017-01-13boost: fixing boost-1.55.0 for gcc-5 (#2822)Andrey Prokopenko2-0/+54
boost-1.55.0 requires patching when compiling with gcc-5. See these threads: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197594 https://svn.boost.org/trac/boost/ticket/10125 Fixes #2821.
2017-01-10Update the boost versions used by openspeedshop. Boost-1.60 to current ↵Jim Galarowicz6-16/+16
latest causes compile errors when building openspeedshop. (#2300) * Update the krell institute products to use the latest features of spack for building on cluster platforms. * Address travis error messages and resubmit the pull request. * Update the contents of openspeedshop package.py so it passes the flake8 tests. * Fix flake8 error-whitespack issue in mrnet package.py file. * Add updates based on spack reviewer feedback. * More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH. * More review related changes. Update MPIOption.append lines and take out xercesc references. * Create a base options function for common openspeedshop base cmake options to reduce redundencies. * Add libxml2+python depends on to get around issues with the libxml2 package file. * Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build. * Fix bad syntax in specifying the boost version range. * Update the version numbers for the krell institute components and tools: cbtf and openspeedshop. * Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
2017-01-10openjpeg: fixes url (#2790)Massimiliano Culpo1-0/+4
2017-01-09Temporary workaround for R concretization bug (#2756)Adam J. Stewart1-2/+1
2017-01-09Added list_url to r-dt package (#1533)sknigh1-0/+1
2017-01-07Get Rid of nobuild, nolink, and alldeps (#2765)Elizabeth Fischer177-495/+499
* Removing the nobuild, nolink, and alldeps dependency types in favor of being explicit. * This will help with maintenance going forward, as adding more dependency types won't affect existing declared dependencies in weird ways. * default deptype is still `('build', 'link')`
2017-01-07Various updates to the NCO package and dependencies (#2639)Adam J. Stewart9-100/+45
* Remove +mpi variant from NCO * Update NCO deps to AutotoolsPackage * Update the other NetCDF packages to AutotoolsPackage * ANTLR has a nolink deptype on java, don't worry about csharp * Remove restrictions from NCO package, fix homepage * Add version 4.6.3 of NCO * Missed AutotoolsPackage for NetCDF-CXX4 * NetCDF tests fail when run in parallel * Remove commented out dependency * Add documentation dependency
2017-01-07Unset PETSC_DIR during installation (#2768)Adam J. Stewart1-1/+11
* Set PETSC_DIR during installation * Move env var unsets to setup_environment * Fix unset var name and number of args
2017-01-07Added needed deps for bbcp (#2773)James Wynne III1-0/+3
2017-01-07Preliminary RPackage class (#2761)Adam J. Stewart170-1205/+176
2017-01-07Fix issues linking hDF5 1.8.14 and below on Ubuntu. (#2772)Todd Gamblin1-1/+15
2017-01-06add conduit 0.2.1 release (#2766)Cyrus Harrison1-1/+2
2017-01-06Add boost 1.63.0 (#2743)Bruno Turcksin1-0/+1
2017-01-06Merge pull request #2740 from jrood-nrel/jonroodGregory Lee1-1/+2
Renaming mkl to intel-mkl
2017-01-06various python package version and dependency updates (#2751)Gregory Lee7-3/+11
* various python package version and dependency updates * various python package version and dependency updates
2017-01-05espressopp: package for the ESPResSo++ software (#2602)Christoph Junghans1-0/+79
* espressopp: package for the ESPResSo++ software This commit adds a package for the ESPResSo++ simulation software. * Move Espressopp package to CMakePackage This commit moves Espressopp package to CMakePackage. Addresses some comments in the PR. * Remove run_tests and changed type of dependencies Addressed some comments from @adamjstewart. Removed global run_tests setting and removed type from many dependencies. Set type for py-mpi4py to 'nolink'. * Updated to last version and fix mpi4py dependency Added latest espressopp version and changed mpi4py (version) dependency for different espressopp versions. * Changed mpi4py version requirements for espressopp Changed py-mpi4py version requirements for espressopp@1.9.4 according to the package build requirements for that version.
2017-01-05Add dependencies and finish the py-tornado package.Matthew Krafczyk34-26/+1200
This adds the following packages: py-backports-shutil-get-terminal-size py-nbformat py-backports-ssl-match-hostname py-pathlib2 py-entrypoints py-pickleshare py-futures py-pip py-ipykernel py-prompt-toolkit py-ipython-genutils py-ptyprocess py-ipywidgets py-simplegeneric py-jupyter-client py-singledispatch py-jupyter-console py-terminado py-jupyter-core py-traitlets py-jupyter-notebook py-wcwidth py-monotonic py-widgetsnbextension py-nbconvert
2017-01-05Added npm, node.js, and Jupyter dependenciesJean-Paul Pelteret10-0/+485
Adds the following packages: node-js py-backports-abc py-functools32 py-pycurl py-vcversione npm py-certifi py-jsonschema py-tornado py-zmq - Added python packages that are dependencies for the Jupyter suite - Update new python packaages to use extension package install function. - Added npm and node-js packages
2017-01-04Standardize package names: lower-case, not Mixed_CASE (#2475)Elizabeth Fischer197-188/+188
* Rename packages * Upcasing depends_on() in packages. * Downcased extends('r') * Fixed erroneously changed URL that had slipped through. * Fixed typo * Fixed link from documentation into package source code. * Fixed another doc problem. * Changed underscores to dashes in package names. * Added test to enforce lowercase, no-underscore naming convention. * Fix r-xgboost * Downcase more instances of 'R' in package auto-creation. * Fix test. * Converted unit test packages to use dashes not underscores * Downcase `r` in the docs. * Update module_file_support.rst Fix r->R for class R.
2017-01-04Intel-mkl provides mklJon Rood1-0/+1
2017-01-04Renaming mkl to intel-mklJon Rood1-1/+1
2017-01-04Use zlib's "fossil" site for old tarballs (#2735)George Hartzell1-4/+5
* Use zlib's "fossil" site for old tarballs Following citibeth's suggestion in #2732, use zlib's "fossil" site (not to be confused with the sqlite team's VCS...) for retrieving old tarballs. Digests for 1.2.{8,10} match and both install for me on CentOS 7. * Use zlib's "fossil" URL as the one true URL Everything seems to be available at zlib's "fossil" URL, so just use it as the one and only url. (and fix a flake8 complaint about a comment)
2017-01-04add package for conduit (#2670)Cyrus Harrison1-0/+312
* add package for conduit * try to fix main conduit docstring * use join_path instead of pjoin * address a few requests in pr #2670 change name of 'github-master' to 'master' change 'docs' variant to 'doc', set default to False remove explicit +shared variant spec for silo and hdf5 deps (in the conduit +shared case) cases since they default to True add reference to static rpath issue (https://github.com/LLNL/spack/issues/2658) * address pr #2670 requests add todos and more info on why variants for deps where selected use python module install python to enable spack activate use .format instead of %s
2017-01-04opencoarrays: new version (#2734)Jeffrey Salmond1-3/+1
* add version 1.8.0 * remove depends_on('cmake') as it is now unecessary * remove 'coarrays' as a virtual package
2017-01-04New package: ccache (#2721)Jean-Paul Pelteret1-0/+44
2017-01-04libpng: Upgrade versions to fix vulnerability. (#2723)Elizabeth Fischer2-7/+15
2017-01-04zlib@1.2.10 and R do not get along, work around it (#2727)George Hartzell1-0/+1
* zlib@1.2.10 and R do not get along, work around it R's configure script has trouble with version numbers > 1.2.9. This works around it by constraining R to 1.2.8. I'm working with some R folk on getting it fixed going forward. * Add adamjstewart's change.
2017-01-03Update to latest zlib version, server no longer provides older version (#2720)Barry Smith1-1/+4
* Update to latest zlib version, server no longer provides older version Funded-by: IDEAS Project: IDEAS/xSDK * Add alternative URL for previous release of zlib
2017-01-02Fix issues when a package provides the same vdep twice. (#2710)Todd Gamblin1-0/+51
* Fix issues when a package provides the same vdep twice. - provides() now adds to a set of provided vdeps instead of a single one. * flake8
2016-12-30Add latest version of gmp (#2695)Adam J. Stewart1-4/+5
2016-12-30Fix Python issue with build failures; Add test case for build failures. (#2687)Todd Gamblin1-0/+37
2016-12-29Concretize preserves deptypes (#2681)Todd Gamblin4-0/+151
Concretization preserves deptypes
2016-12-28Directive inheritance: laziness for the win (#2623)Massimiliano Culpo4-5/+24
* inheritance of directives: using meta-classes to inject attributes coming from directives into packages + lazy directives * _dep_types -> dependency_types * using a meta-class to inject directives into packages * directives are lazy fixes #2466 * directives.py: allows for multiple inheritance. Added blank lines as suggested by @tgamblin * directives.py: added a test for simple inheritance of directives * Minor improvement requested by @tgamblin CMakePackage: importing names from spack.directives directives: wrap __new__ to respect pep8 * Refactoring requested by @tgamblin directives: removed global variables in favor of class variables. Simplified the interface for directives (they return a callable on a package or a list of them).
2016-12-28init yorick package (#2635)Thierry1-0/+81
* init yorick package * attempt at picking up SPACK's compiler choice, todo ~X variant. * sphinx docstring error ? * version# tarball, ~X default, docstring fix * sphinx docstring fix(?)
2016-12-27Cleanup post luafilesystem version de-underscoring (#2683)George Hartzell1-3/+3
The upstream luafilesystem tarball/version had a wayward/inconsistent underscore in their more recent version tag. The played badly with our package fetching machinery (due to recent changes?). Upstream cleaned up their bit which required some touchups here. - updated the url - updated the version (digest) - updated the format statement for the path to the rockspec.
2016-12-27Adds catch, cppunit, spdlog, tinyxml(1 and 2), google benchmark (#2627)Mayeul d'Avezac7-0/+264
* Adds catch, cppunit, spdlog, tinyxml(1 and 2), google benchmark Tinyxml comes in two flavors, 1 and 2. Each comes in several versions... So they cannot be easily united into a single package. * Use CMakePackage and friends, add copyright Also eleminate debug/release variants, since it no longuer fits in the CMakePackage format. * Remove unnecessary url * spdlog now has tagged releases * Remove unnecessary url argument * Fewer quotes in cmake args, because magic * Incorrect base class for tinyxml
2016-12-27Update wx to 3.1.0 (#2641)Michael Kuhn1-5/+12
2016-12-27Ensure that every file in Spack has a license (#2659)Adam J. Stewart34-25/+680
* Ensure that every package has a license Also fixes URLs with http://http:// doubled. This is a continuation of #2656. * Add license to every file in Spack * Make sure Todd is the author of all packages * Fix flake8 tests * Don't license external Sphinx docs * Don't display licenses in tutorial example packages Also fixes typos and converts command-line examples from tcsh to bash, which is more common
2016-12-25Update py-cython with new pypi.io url and new version (#2650)Matthew Scott Krafczyk1-1/+3
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
2016-12-25Update the texlive distro digest. (#2679)George Hartzell1-1/+1
sigh.
2016-12-25go: fixed GOROOT_BOOTSTRAP without workarounds (#2671)Massimiliano Culpo2-9/+5
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.
2016-12-19Update gdal to 2.1.2 (#2643)Michael Kuhn1-2/+3
2016-12-19Various improvements to H5hut (#2636)Adam J. Stewart1-33/+38
2016-12-19moab: 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.
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