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2017-10-26minife: version bump to v2.1.0 (#5985)Christoph Junghans1-21/+6
2017-10-26Laghos: new package (#5956)Abhinav Bhatele2-0/+64
2017-10-26sw4lite: fix build errors and add variants (#5944)Abhinav Bhatele1-4/+42
* sw4lite: fix build errors and add variants * sw4lite: change linking against blas and lapack * change order of blas and lapack * satisfy flake8 requirements * Update package.py
2017-10-26Customization of the Paraview module file to its nonstandard directory ↵Jon Rood1-0/+12
structure (#5799) * Add the custom paraview lib directory structure to the library paths in the paraview module file. * Fixing flake8 issues. * Checking if lib64 exists for paraview module file generation, else use lib. * Fixing more flake8 problems I introduced.
2017-10-26flang: fixed llvm dep (#5948)Christoph Junghans1-3/+9
* flang: fixed llvm dep * add support for llvm-5 * Update package.py * Update package.py
2017-10-26Add option to install clang python bindings to llvm (#5774)Johann Klähn1-0/+7
2017-10-25Make clang use libc++ by default (#5943)Ondřej Čertík1-1/+4
Since LLVM 3.9 Clang can use the libc++ library by default using the CLANG_DEFAULT_CXX_STDLIB cmake configuration variable, without having to specify the -stdlib=libc++ option on the clang++ command line. This commit makes clang++ use libc++ by default for LLVM 3.9 and later if the libcxx variant is on. Fixes #5942.
2017-10-25adding miniTri miniapp (#5935)mmwolf1-0/+63
2017-10-25boost: remove duplicate patch (#5934)Omar Padron2-55/+2
2017-10-25tweak opencv version (#5623)Jimmy Tang1-1/+1
2017-10-25Update for 'netcdf'. (#5819)Sergey Kosukhin1-82/+135
2017-10-25delly2: new package (#5820)Audrey Thoma1-0/+65
2017-10-25Zlib gets a 50-60% performance win when compiled with -O2 (#5838)David Hows1-0/+4
Chasing a performance regression has lead me to this change, going from default optimization gives a significant performance win. The sweet spot for zlib is apparently `-O2`, both `-Ofast` and `-O3` are slightly worse (regression is about 3% compared with `-O2) in my testing. Happy to share my methodology with people so we can benchmark on a wider variety of systems.
2017-10-25Update for 'eccodes'. (#5899)Sergey Kosukhin3-20/+102
2017-10-25Add package for scalpel@0.5.3 (#5901)George Hartzell1-0/+101
* Add package for scalpel@0.5.3 Scalpel's a bit of a mess, it expects it's users to just unpack the tarball, build it in the resulting directory and install that directory onto their PATH. My install step recapitulates this into prefix.bin. The alternative was rewiring their scripts (perl), which use `FindBin` and expect things to be located in the same dir that the script itself is. Sigh. Lightly tested on CentOS 7. * Flake8 cleanup * Additional flake8 cleanup
2017-10-25adding perl-bio-perl and dependencies (#5845)Audrey Thoma11-0/+428
* perl-bio-perl and dependencies * minor fixes * condensing code * fixing doc error
2017-10-25Update for 'cdo'. (#5947)Sergey Kosukhin1-53/+68
2017-10-25bwa: add 0.7.17 (#5902)Eric1-0/+4
* bwa: add 0.7.17 * bwa: add 0.7.13
2017-10-25Add old version to bcftools (#5907)George Hartzell2-0/+9
* bcftools v1.2 and htslib v1.2 * dependency change - only require dependencies for v1.2
2017-10-25py-xlsxwriter: new package (#5918)Audrey Thoma1-0/+35
2017-10-25adding bedtools2 v2.23.0 (#5911)George Hartzell1-0/+1
2017-10-25Parallel fix sbangs (#5910)George Hartzell1-0/+16
* Added procedure to edit sbangs of the parallel perl scripts. * Specify the types of perl dependency Adding ", type=('build', 'run')" to the dependency declaration to clarify when and how perl is required * flake8 cleanup
2017-10-25adding perl-moose and dependencies (#5912)Audrey Thoma29-0/+1033
* adding perl-moose and dependencies * added missing dependency * fixed flake8 errors
2017-10-25Added Hypre Dependency to mfem+hypre (#5929)Robert Pavel1-0/+1
Added missing hypre defendency from mfem's hypre-enabled version
2017-10-25r-geneplotter: Create new package. (#5924)lingnanyuan1-0/+42
2017-10-25r-gridextra: Update version to 2.3 (#5915)lingnanyuan1-1/+3
2017-10-25r-geiger and dependencies (#5933)Audrey Thoma4-0/+151
2017-10-25r-rbgl: Create new package. (#5931)lingnanyuan1-0/+38
2017-10-25r-variantannotation: created new package (#5932)Yifan Zhu1-0/+54
2017-10-25r-gseabase: Create new package. (#5930)lingnanyuan1-0/+43
2017-10-25r-bsgenome: created new package (#5928)Yifan Zhu1-0/+47
2017-10-25r-lsei: new package (#5926)Yifan Zhu1-0/+41
2017-10-25r-yarn: created new package (#5925)Yifan Zhu1-0/+53
2017-10-25r-formula: Update version to 1.2-2 (#5923)lingnanyuan1-1/+3
2017-10-25r-quantro: created new package (#5922)Yifan Zhu1-0/+49
2017-10-25r-scales: Update url. (#5921)lingnanyuan1-1/+2
2017-10-25r-doparallel: added list_url and version 1.0.11 (#5920)Yifan Zhu1-0/+2
2017-10-25r-hmisc: Create new package. (#5919)lingnanyuan1-0/+53
* r-hmisc: Create new package. * Correct format.
2017-10-25r-openssl: changed homepage url to the CRAN package homepage, added list_url ↵Yifan Zhu1-1/+3
and added version 0.9.7 (#5848)
2017-10-25Glibc 2.26 does not provide xlocale.h (#5862)Praveen C2-0/+17
2017-10-25gdbm: pass in proper CPPFLAGS (#5893)Ondřej Čertík1-1/+6
The problem was that the configure script was not using spack's compiler wrappers. We now pass the proper compiler wrapper using the CC argument explicitly. Fixes #5892.
2017-10-24Add a new package for AMG and fix build issues in the amg2013 package (#5909)Abhinav Bhatele2-12/+90
* amg2013: fix build issues * amg: add new package * Update package.py * amg2013: standardize option name * amg: standardize option names
2017-10-24hypre: make mpi dependency optional (#5905)Ondřej Čertík1-5/+10
2017-10-24Added Spackage for SW4Lite proxy (#5917)Robert Pavel1-0/+54
Added Spackage for C version of SW4Lite proxy. Fortran will follow once race conditions involving .mod files are resolved
2017-10-24slepc and petsc version updates (#5863)Denis Davydov2-3/+2
slepc: add 3.8.0 petsc: no longer prefer 3.7.7
2017-10-24r-minfi: created new package (#5887)Yifan Zhu1-0/+63
2017-10-24Add a package: thrust. (#3729)健美猫1-0/+40
2017-10-24r-nlme: added list_url and version 3.1-131 (#5890)Yifan Zhu1-0/+2
2017-10-24r-genomicalignments: created new package (#5785)Yifan Zhu1-0/+49
* r-genomicalignments: created new package * r-genomicalignments: using git repo source instead
2017-10-24r-reshape: created new package (#5889)Yifan Zhu1-0/+38