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2017-09-25Fix Protobuf URLs (#5373)Axel Huebl1-3/+15
The default implementation of Package.fetch_remote_versions will take a URL like https://github.com/google/protobuf/archive/ and automatically search https://github.com/google/protobuf/releases/ for new package versions. In the case of protobuf the release/ path contains release artifacts for a version and the archive/ path contains the desired source. Since both are associated with the version, and Package.fetch_remote_versions only stores one URL for a given version, the two paths are in conflict; previously the URL returned for a given version was arbitrarily chosen between the two paths. This updates the definition for the Protobuf package to always search for URLs in https://github.com/google/protobuf/archive/
2017-09-25lammps: add support of latte package (#5446)Christoph Junghans2-1/+35
2017-09-25Add info for lmod@7.7 and lmod@7.6.14 (#5450)George Hartzell1-0/+2
Lightly tested on CentOS 7
2017-09-25add assimp package. link against it in dealii (#5463)Denis Davydov2-0/+56
2017-09-24New version for mosh1.3.2 (#5448)George Hartzell2-1/+2
Required an update to the protobuf digest value, which seems to be amongst the set creamed by GitHub's change.
2017-09-24llvm: patch lldb for gcc-7 (#5239)Andrey Prokopenko2-0/+13
2017-09-23hdf5: fix macOS build by not using numactl (#5458)Denis Davydov1-1/+4
2017-09-23parsplice: add version 1.1 (#5461)Christoph Junghans1-1/+2
2017-09-23blas_lapack: add multithreading variant consistent in all implementations. ↵Denis Davydov5-22/+67
(#5340) * blas_lapack: add multithreading variant * elemental: update * intel-mkl: extend to macOS * rename multithreading to threads * intel-mkl: avoid long lines * intel-mkl: make one install error a conflict * openblas: fix a minor bug in the test
2017-09-23r-rsqlite: Update version to 2.0. (#5444)lingnanyuan1-3/+10
* pr-quantities: add version & py-numpy conflict (#5307) * r-rsqlite: Update version to 2.0
2017-09-23r-bh: update version. (#5442)lingnanyuan1-2/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-bh: Update version to 1.65.0-1
2017-09-23r-memoise: update version. (#5440)lingnanyuan1-2/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-memoise: Update version to 1.1.0
2017-09-23r-tibble: update version. (#5439)lingnanyuan1-3/+4
* pr-quantities: add version & py-numpy conflict (#5307) * r-tibble: Update version to 1.3.4
2017-09-23r-bit: new package. (#5436)lingnanyuan1-0/+34
* pr-quantities: add version & py-numpy conflict (#5307) * r-bit: Create new package.
2017-09-23r-assertthat: update version to 0.2.0 (#5435)lingnanyuan1-1/+2
* pr-quantities: add version & py-numpy conflict (#5307) * r-assertthat: Update version to 0.2.0
2017-09-23r-preprocesscore: created new package (#5434)Yifan Zhu1-0/+35
2017-09-23r-affyio: created new package (#5433)Yifan Zhu1-0/+37
2017-09-23r-xvector: created new package (#5432)Yifan Zhu1-0/+41
2017-09-23superlu-dist: fix has after 09/17/2017 update (#5457)Denis Davydov1-2/+2
2017-09-22tmux: add version 2.5 (#5449)George Hartzell1-0/+1
2017-09-22Ack: add version 2.18 (#5445)George Hartzell1-0/+1
2017-09-23Add info for httpie@0.9.9 (#5451)George Hartzell1-0/+1
Lightly tested on CentOS 7.
2017-09-23Add info for lftp@4.8.1 (#5452)George Hartzell1-0/+1
Lightly tested on CentOS 7.
2017-09-22Update git to @2.14.1, requires pcre+jit variant (#5430)George Hartzell2-1/+13
Update the git package to git@2.14.1. This requires a pcre that has been built with `--enable-jit`, so this adds a variant to pcre to support that and arranges so that git versions before 2.14 depend on pcre and git 2.14 and after depend on pcre+jit.
2017-09-22git-lfs: add 2.2.1 and 2.3.0 (#5429)George Hartzell1-0/+2
2017-09-22emacs: add version 25.3 (security update) (#5447)George Hartzell1-0/+1
25.3 is a security update. Info here: https://lists.gnu.org/archive/html/info-gnu/2017-09/msg00006.html Build both +X and ~X on CentOS 7 and lightly tested.
2017-09-22plumed: fixed possible linking issue (#5425)Massimiliano Culpo1-1/+6
Due to the logic in configure.ac, we may be using both the system linker (LD_RO='ld -r -o') and the linker tied to the compiler (LD=$CXX). This may produce weird link-time errors when the two executables are not the same. The PR works around the issue disabling 'ld -r'
2017-09-22PMIx: add PMIx package to Spack (#5426)Howard Pritchard1-0/+71
Open MPI has been relying on versions of PMIx since the 2.0.0 release. Although the embedded version can be used, it makes more sense long term for Spack to know about the PMIx package, and to build Open MPI against PMIx as an external package. There are other software components that may eventually be reliant on PMIx including MPICH, GASNet, the OpenSHMEM reference implementation, etc. This is also partly motivated by the desire to have ECP ST projects to be released through Spack. Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-09-22Version fixes for py-csvkit (#5393)sknigh4-3/+7
2017-09-21Add package py-memory-profiler (#5413)healther1-0/+37
* add package memory profiler * fix FIXME
2017-09-21r-s4vectors: created new package (#5419)Yifan Zhu1-0/+43
* r-s4vecors: created new package * Update package.py * edited according to flake8
2017-09-21Update pic/shared variants for hdf5, python, silo (#5423)Mike Pozulp3-0/+16
2017-09-21r-mpm: new package. (#5416)lingnanyuan1-0/+38
2017-09-21OpenMPI: add 2.1.2 bug fix release (#5418)Howard Pritchard1-2/+3
2017-09-21Add cpu_target variant to openblas (#5090)healther1-1/+9
2017-09-21Use trusted/historic site for texlive installer (#5347)George Hartzell1-8/+11
* Make texlive untrusted TeXLive updates their installer without changing its name. We've been playing keep-up with them, but I'm proposing it's not worth it. I seem to end up installing it '--no-checksum' anyway. This commit updates the package to make that approach official, removing the checksum, adding a note to the description and a bigger note/comment inthe package body. * Pull installer from stable source (packages are still *live*) This pulls the installer script from the "historic" repository. It appears to be stable, so that we can use a checksum with it (one hopes, time will tell). The installer still pulls the packages from the live repos so installations aren't reproducible.
2017-09-21fix install method of cereal (#5094)healther1-9/+2
* removed unnecessary install method from cereal * attempt to fix flake8 error * adjusted install method * add CMake options instead of manually patching stuff * flake8
2017-09-21r-zlibbioc: new package (#5399)Yifan Zhu1-0/+38
2017-09-21r-biocinstaller: added version 1.26.1 (#5406)Yifan Zhu1-2/+4
2017-09-21dealii: add cuda support (#5402)BenBrands1-0/+17
2017-09-20Opencv: fix dependencies and variants (#5232)Brian Van Essen1-1/+2
Fixes #5159 * Added dependency on google protobuf when using v3.3.0. * Set default for variant core to be true.
2017-09-20latte: add v1.0.1 (#5403)Christoph Junghans1-0/+1
2017-09-20r-biobase: new package (#5398)Levi Baber2-11/+43
Add r-biobase package. Remove explicit R dependency from r-biocgenerics package (since it is an instance of RPackage). Update version for r-biocgenerics and remove github versions.
2017-09-20Add info for mono@5.4.0.167 (#5405)George Hartzell1-0/+1
2017-09-20r-survival: updated to version 2.41-3 (#5409)Yifan Zhu1-1/+3
2017-09-20[WIP]: Sambamba new package (#5304)George Hartzell2-0/+63
* First draft package for sambamba Depends on the ldc package (#5279) that alalazo's working on. It requires a patch to the Makefile because one of ldc's library functions mentions dlopen. I *think* that ldc should be handling this. See the discusssion in #5279. It also requires a "static" ldc. Again, see #5279. Finally, it needs "undeaD" as a resource, but I'm guessing at the appropriate release. See https://github.com/lomereiter/sambamba/issues/312. * alalazo renamed the shared_libs variant, keep up...
2017-09-20Update recipe for cgns to avoid build warnings/errors: (#5382)Kelly (KT) Thompson1-10/+3
+ The recipe for cgns seems to be wrong. CMake complains about variables set but not used (`HDF5_NEEDS_ZLIB`, `HDF5_NEEDS_MPI` and `HDF5_NEEDS_SZIP`) and fails to find HDF5. + This change set removes these variables from the cmake configure line, replacing them with `'-DHDF5_DIR=%s' % spec['hdf5'].prefix` + cgns also has trouble with parallel make, so I set `parallel = False`.
2017-09-20Rm arpack parpack (#5391)Mark C. Miller3-144/+1
* fixes #967 * Version bump to 0.9.1 - Bugfixes for spack find - 0.9.1 can read specs from current develop. * Don't assume spack is in the path when building docs. * fixing build issues for gcc on osx * reverting inadvertent change on develop * fixing typesetting of bsws description * very minor update to RTD docs footer to ref github contributors * Revert "very minor update to RTD docs footer to ref github contributors" This reverts commit c40d75da7f3b918350a263e7a9ef34df56b7fb01. * switch fastmath to depend_on arpack_ng; remove arpack/parpack
2017-09-20added Intel 2018 tools (#5404)Gregory Lee2-0/+8
2017-09-20mirdeep: new package (#5302)Audrey Thoma10-0/+387
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