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2018-08-02Package py-biom-format fixes (#8727)Levi Baber1-1/+2
* py-biom-format: needs py-setuptools at runtime * py-biom-format: needs py-pyqi
2018-08-02New package: GRNBoost (#8763)Yifan Zhu1-0/+61
2018-08-02Replace pkg-config dependencies with virtual (#8783)Michael Kuhn9-14/+14
Several packages specified pkg-config as a dependency, which is a specific implementation of the pkgconfig virtual. Most packages do not request a specific implementation. The current concretizer may choose a different implentation of pkgconfig for the nonspecific dependents, which conflicts with the request for pkg-config. This replaces all requests for a specific implementation of pkgconfig with the virtual package as a temporary solution to the issue.
2018-08-02package neovim: add info for version 0.3.1 (#8866)Matthias Wolf1-0/+1
2018-08-02Update homepage for laghos (#8864)Adam J. Stewart1-1/+1
2018-08-02Adding lazy property python module (#47) (#8867)Matthias Wolf1-0/+37
2018-08-02sz: fix checksum for 2.0.2.0 (#8868)Michael Kuhn1-1/+1
2018-08-02Trilinos: Update rules for superlu-dist version compatibility. (#8851)Kelly (KT) Thompson1-0/+1
2018-08-02Update and Bugfix for pexsi/package.py (#8822)Takayuki Kobayashi1-20/+25
* Update and Bugfix for pexsi/package.py 1. pexsi@0.10.2 is not compatible with superlu-dist@5.4.0 due to [Change LargeDiag to LargeDiag_MC64; Add LargeDiag_AWPM](https://github.com/xiaoyeli/superlu_dist/commit/d7dce5a3488f80645023ab8431d82399e5546ebf). 2. In the 'edit' phase, '@MPICXX_LIB' must be substituted before '@MPICXX' is substituted. * change dict to list of tuples Use a list of tuples to remember the order of `substitutions`. * Update package.py * Update package.py
2018-08-02added py-setuptools as dependency (#8843)Douglas Duckworth1-2/+3
* added py-setuptools as dependency * more changes
2018-08-02CMake: patch for NAG. (#8869)Sergey Kosukhin2-0/+12
2018-08-02adios2: add 2.2.0 (#8871)Michael Kuhn1-5/+17
This also enables the bzip2 and zfp variants. The sz variant is currently broken.
2018-08-02netcdf-fortran: enforce autoreconf when building with NAG. (#8844)Sergey Kosukhin2-0/+35
* netcdf-fortran: enforce autoreconf when building with NAG. * netcdf-fortran: patch the configure script instead of running autoreconf to get rid of additional dependencies. * netcdf-fortran: add comment for the patch.
2018-08-02suite-sparse: add version 5.3.0 (#8837)Geoffrey Oxberry1-1/+2
2018-08-01openblas: add version 0.3.2 (#8833)Geoffrey Oxberry1-0/+1
2018-08-01Dia needs access to gettext and pkg-config. (#8840)Kelly (KT) Thompson1-0/+2
When using spack on a ubuntu baseline system, I was unable to build dia with adding these build dependencies on gettext and pkg-config.
2018-08-01Small patch for netlib-lapack. (#8854)Sergey Kosukhin2-0/+18
2018-08-01Conflict for cmake 3.11.x and Intel. (#8855)Sergey Kosukhin1-0/+3
2018-08-01lmod: fix use of custom separator in prepend_path etc. (#8737)Stephen Herbein1-0/+44
fixes #8736
2018-07-31lmod: add version 7.8 (#8838)Geoffrey Oxberry1-0/+1
2018-07-30slepc: add blopex variant (#8820)Geoffrey Oxberry1-0/+14
2018-07-30Add extra_rpaths to OpenMPI wrappers (#8687)Jon Rood1-0/+7
If the OpenMPI build finds the infiniband drivers in /usr/lib64, it adds -Wl,-rpath -Wl,/usr/lib64 to the OpenMPI wrappers. If the wrappers are using a compiler outside of /usr, and the OpenMPI wrappers are used to build software outside of Spack, they will rpath /usr/lib64 into the executable which then has GLIBC, GLIBCXX runtime errors due to it picking up GCC libraries in /usr/lib64. This adds the directories specified in "extra_rpaths" to the OpenMPI wrappers, which allows them to use the correct compiler when invoked outside of Spack builds.
2018-07-30GSL: 2.5 is a new version. (#8827)Kelly (KT) Thompson1-0/+1
2018-07-29libunwind: document platform=darwin conflict (#8824)Geoffrey Oxberry1-0/+3
2018-07-27added Tasmanian versions 5.1 and development, enabled the Tasmanian options ↵Miroslav Stoyanov1-3/+90
through +~ flags (#8804)
2018-07-27Skip update check. (#8683)健美猞猁1-0/+5
* Skip update check. * mkefile -> makefile. * Fix emboss.
2018-07-27gcc: Add 8.2.0 (#8813)Michael Kuhn1-0/+1
2018-07-26py-numpy: Add CPATH in modulefile (#8466)Oliver Breitwieser1-3/+11
Also fix setup_dependent_package to include the ".egg-less"-include path. Change-Id: I06e66a505ece25cba8896f47e69a5be374bac6d2
2018-07-26Updated llvm to version 6.0.1. The previous 6.0.0 had an incorrectly … (#8801)Neil Flood2-0/+20
* Updated llvm to version 6.0.1. The previous 6.0.0 had an incorrectly declared symbol, discussed at https://reviews.llvm.org/D44140, which, amongst other things, broke py-numba. This version works fine with py-numba. * Flag the conflict between py-numba and llvm@6.0.0 * Removed a single trailing space to satisfy checks
2018-07-26sz: new version 2.0.2.0 (#8786)Sheng Di1-4/+11
2018-07-26hdf5: Fix build with %gcc@8 (#8788)Michael Kuhn1-0/+4
2018-07-26halc: Create new package. (#8795)lingnanyuan1-0/+48
* halc: Create new package. * fix flake8 error. * Modification
2018-07-26FTGL package workarounds (#8812)Hadrien G2-0/+21
* FTGL package workarounds * Remove blank line * Only require doxygen at build time
2018-07-26AMReX: update package.py (#8697)mic841-49/+51
2018-07-26Templight package (#8782)Hadrien G3-0/+247
* First draft of a templight recipe * Let's be explicit for now, we can be clever later on * The clang6 version does not work, drop it * Reorder FIXMEs more logically * Add patch for current templight develop branch * Create an artificial stable release of templight * Take some additional inspiration from llvm package * Added the templight supporting tools * Remove old notes from the no-url branch * Avoid unnecessary join_path
2018-07-26hmmer: added version 3.2.1 & updated URL (#8787)Simon Flood1-9/+2
Add HMMER 3.2.1 and updated URL then removed url_for_version function as no longer required - all HMMER downloads available from updated URL.
2018-07-26papi: Update to 5.6.0 and fix build with %gcc@8 (#8796)Michael Kuhn1-0/+5
2018-07-26Add package DMTCP (#8808)Mario Melara1-0/+36
2018-07-26mfem: mfem-3.3-3.4-petsc-3.9.patch is not needed for latest develop version ↵Satish Balay1-1/+1
(#8809)
2018-07-25intel-tbb: Add `tm` variant to disable transactional memory. (#8799)Mark W. Krentel2-0/+21
* intel-tbb: Add variant `tm` to disable transactional memory. Some AMD or very old Intel systems don't support transactional memory. This commit adds a variant `tm` that defaults to `True`, but can be switched off to allow running on those systems.
2018-07-25Add docs on new top-level VCS attributesAdam J. Stewart1-4/+3
2018-07-25Unit test fixesAdam J. Stewart4-13/+1
2018-07-25Further improvements to version parsingAdam J. Stewart33-60/+38
2018-07-25All git URLs end in .gitAdam J. Stewart15-19/+19
2018-07-25Replace git=git with explicit branch namesAdam J. Stewart29-33/+32
2018-07-25Add top-level attributes for git R-Z packagesAdam J. Stewart71-194/+204
2018-07-25Add top-level attributes for git R (Bioconductor) packagesAdam J. Stewart141-360/+307
2018-07-25Add top-level attributes for git M-P packagesAdam J. Stewart104-343/+287
2018-07-25Add top-level attributes for hg, svn, and git A-L packagesAdam J. Stewart152-486/+461
2018-07-25tests: add checks and tests for consistent version() argumentsTodd Gamblin7-30/+31
- Previously, Spack didn't check the arguments you put in version() directives. - So, you could do something like this, where there are arguments for a URL fetcher AND for a git fetcher: version('1.0', md5='abc123', git='https://foo.bar', commit='feda2343') - Now, we check the arguments before constructing a fetcher, to ensure that each package has *only* arguments for a single type of fetcher. - Also added `test_package_version_consistency()` to the `package_sanity` test, so that all builtin packages are required to have valid `version()` directives.
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