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2018-05-28plumed: added versions 2.4.1 and 2.3.5 (#8297)Massimiliano Culpo1-0/+2
2018-05-28yambo: added versions 4.2.2 (#8298)Massimiliano Culpo1-0/+1
2018-05-26Add JasPer 2.0.14 (#8207)Adam J. Stewart1-14/+77
* Add JasPer 2.0.14 * Remove no longer necessary patch * Explicitly disable generation of documentation * Re-add support for JasPer 1.900.1, add GDAL patch * Remove GDAL patch
2018-05-26Add GDAL 2.3.0 (#8263)Adam J. Stewart2-46/+592
* Add GDAL 2.3.0 * Add missing dependencies, change default variants, and add links * GDAL requires old hacked version of JasPer * Move JasPer patch to GDAL
2018-05-26Fix compilation of FYBA with GCC 6 (#8273)Adam J. Stewart2-0/+22
2018-05-26Fix gettext: Problem with libxml2 (#8132)Elizabeth Fischer1-1/+3
* See https://github.com/spack/spack/issues/2882 * code review * Correctly access lib directory
2018-05-26Fix OpenCV JasPer disable (#8287)Corey McNeish1-10/+10
The recipe previously did not include -DWITH_JASPER Other edits: * BUILD_IPP_IW is BUILD instead of WITH; it was in a different section of the CMakeLists.txt. Move it to the top * Several options were missing :BOOL, add them * -DWITH_ZLIB doesn't actually exist as an option, at least in the latest version.
2018-05-25Added new package Camellia. (#8190)Nate Roberts1-0/+61
* Added new package Camellia. * Fixed an issue with a missing blank line. Added a couple more Trilinos packages (things I expect to depend on eventually). * Fixed a couple issues raised by @adamjstewart. * Specified 4.9.2 as the supported MOAB version. 5.0.0 causes build issues on Macs during the link of Camellia's drivers. The issue is that we end up with -framework -lAccelerate in the link line, where it should read -framework Accelerate, I believe. I'm not sure where this comes from, but 4.9.2 does not have this issue. * Trimmed slightly the Trilinos requirements. Also deleted a blank line that had spaces in it because the Travis-CI thing didn't like that. * Reduced length of MOAB description (Travis-CI complained). * Reduced the MOAB line further; didn't quite get there last time! This is to satisfy Travis-CI's requirement that the description be less than 80 characters long (E501). * Put in my GitHub handle, in place of an allusion to my email address. Also added a new argument for Camellia build, and made the MOAB description longer (thanks to @adamjstewart's note that long lines are allowed so long as they are not split). * Added MPI dependency. Added explicit OFF for MOAB enablement when ~moab. Swapped order of variant and version.
2018-05-25repeatmasker: fix bin location and dependency (#8286)Levi Baber1-1/+2
2018-05-25flang: add non-develop version (#8276)Andrey Prokopenko1-1/+2
2018-05-25perl-text-soundex: new package (#8279)Levi Baber1-0/+37
* perl-text-soundex: new package * perl-text-soundex: formatting
2018-05-25hdf5: add 1.10.2 (#8274)David Guibert1-0/+1
2018-05-24Add Tophat v2.1.2, fixes automake issues (#8266)George Hartzell1-1/+6
* Add Tophat v2.1.2, fixes automake issues The Tophat team merged the patch from https://github.com/spack/spack/pull/8244 and release v2.1.2 This change requires the old automake if you're building the older release and is relaxed about the automake it requires if you're building the v2.1.2 release. Building v2.1.1 and v2.1.2 works on a CentOS 7 system, I don't have the necessary bit to actually test the resulting binaries. Here's the commit note from the change that was ultimately merged upstream. Fixes #8025 > Tophat was failing to build with automake@1.16.1, it worked with the > older automake@1.15.1. This commit adds a patch to Tophat's > src/Makefile.am which cleans up a few things. The result builds > successfully with both automake@1.15.1 and automake@1.16.1. I have no > way to check that the resulting builds Do The Right Thing. > > It changes two things: > > the original Makefile.am had a rule for $(SAMPROG) with no > actions, and since there was a directory there with a tempting name > the newer automake was trying to do something with it, but lacked > the appropriate clues. Since that target is actually made as a side > effect of making the library (sigh...), it seems to work to just > give that rule something harmless to do (the Peter Principle > triumphs again...). > > a bunch of the targets need a libtophat.a and libgc.a; the older > automake was probably able to guess what to do given the list of > sources but the newer automake apparently won't make the necessary > assumptions. This patch wires up a simple rule and cleans up the > appropriate dependencies so that things work. > > While it may appear that I'm someone who understands automake, keep in > mind that I only play such a person on a TV reality show. YMMV. * Remove extraneous when constraint
2018-05-24Added gsl dependency to pnfft (#8255)Luca Heltai1-0/+1
2018-05-24Fix missing spack.compiler import (#8240)Michael Kuhn1-0/+1
Fixes: #8258 #8090 altered import behavior so that import spack no longer provides access to many other Spack modules. This addresses a case which depended on the prior behavior and was not updated as part of #8090. This particular import error only came up when users were setting compiler flags on specs. See also: #8194
2018-05-24kokkos: update kokkos spackage to add current host/gpu architectures. (#8226)Geoff Womeldorff1-1/+49
* kokkos: update kokkos spackage to add current host/gpu architectures. * kokkos: simplify host/gpu architecture selection and make intent of arg population logic more clear. * kokkos: mollify flake8. * Make strings and logic more pythonic. Add error for GPU arch without CUDA. * kokkos: simplify conflicts behaviour. make args population more pythonic. * kokkos: move gpu values to list for use in variant and conflicts checking. * kokkos: How fortunate the man with None. * kokkos: fix gpu_arch conflict loop error. add conflict to guard against +cuda and 2.5.00:develop versions, until kokkos issue #1296 is resolved. * kokkos: mollify flake8. * kokkos: add descriptive message to version conflict with +cuda.
2018-05-24Charm++: Add possibility to build git version (#8260)Matthias Diener1-1/+7
2018-05-24Add msgpack-c 3.0.1 (#8264)Sajid Ali1-1/+2
* new file: cpp-3.0.1.tar.gz modified: package.py * deleted: cpp-3.0.1.tar.gz * remove whitespace
2018-05-24trf: make executable (#8265)Levi Baber1-0/+2
2018-05-24openfoam-org: add v2.4.0 (#7850)Chris Hadjigeorgiou2-11/+118
Add 2.4.0 changes
2018-05-24Fix MD5 hash for opencv 3.2.0 and 3.1.0 release (#8241)jkelling1-2/+2
2018-05-23Add info for datamash@1.3 (#8261)George Hartzell1-0/+1
2018-05-23Add kealib 1.4.7 (#8235)Adam J. Stewart2-7/+83
* Add kealib 1.4.7 * Fix out-of-source builds * Remove username from kealib hg clone
2018-05-23Add PROJ 5.0.1 (#8233)Adam J. Stewart1-3/+22
* Add PROJ 5.0.1 * proj-datumgrid resource must be placed in nad directory
2018-05-23mvapich2: added a proper libs attribute (#8253)Massimiliano Culpo1-0/+12
2018-05-23Add pkgconf 1.4.2 (#8256)Adam J. Stewart1-3/+7
2018-05-23Add ncurses 6.1 (#8257)Adam J. Stewart1-1/+2
2018-05-23charm: Update install script (#7291)Edward Kim1-45/+94
* charm: Update install script * Addressed PR comments * Removed destination and suffix variants * Added back parallel support
2018-05-23gromacs: added version 2018.1 (#8251)Massimiliano Culpo1-0/+1
2018-05-23cgal: added version 4.12 (#8252)Massimiliano Culpo1-0/+1
2018-05-23Update BookLeaf_Cpp and Typhon packages. (#8249)Tim Law2-0/+2
2018-05-23Add latest versions of bazel (#8250)Leonhard Reichenbach2-3/+130
2018-05-23Package/mirdeep/fix for new url take2 (#8247)Sinan1-4/+4
* rename: mirdeep -> mirdeep2 * fixes for new url
2018-05-22Create new package: memkind (#8242)Leonhard Reichenbach1-0/+68
* Create new package: memkind * some style changes * fix type of numactl dependency * fix flake8 errors * use patch() instead of a custom build phase
2018-05-22Add py-docopt package (#8236)Adam J. Stewart1-0/+38
2018-05-22subread: added version 1.6.2 (#8239)Massimiliano Culpo1-0/+1
2018-05-22CUDA 9.2 (#8238)Axel Huebl2-7/+11
Add the latest CUDA release, v9.2 and updated CUDA Compatibility Matrix
2018-05-21Update GlobalArrays package to new releases (#7840)Tim Stavenger2-279/+45
* update globalarrays package to current releases * rename class to Globalarrays to match package folder * rename bytes to int64, minor cleanup of descriptions * int64 False by default * remove reference to external as we aren't supplying paths, and use args.append() * correcting args.append syntax * add conflicts
2018-05-21gdbm: Get working on CentOS5 and Other Older Systems (#8134)Elizabeth Fischer1-1/+9
* Fix #7691 * flake8 * code review
2018-05-21netcdf-cxx4: Update to use CPPFLAGS (#8148)Elizabeth Fischer2-0/+6
* Fix bug; don't know why this ever worked in the first place. * Add fix to netcdf-fortran too; flake8 * Simplify configure_args() * netcdf-fortran: simplify that too
2018-05-21Create new package: fastgbs and its dependency platypus. (#8174)lingnanyuan2-0/+97
* pushing partially done recipe for fast-gbs and platypus * modify platypus * change header * fast-gbs: change dependency type. * modify dependency type. * modify dependency type. * fast-gbs: Change dependency type to run.
2018-05-21r-cghflasso v0 2 1 - new package (#8177)peetsv1-0/+36
* py-pyfaidx: adding new package * updating the url * r-cghflasso v0.2-1 new package * correcting copy/paste error * adding list_url
2018-05-21Add urls into cbtf* and openspeedshop* package files and update the release ↵Jim Galarowicz8-112/+121
versions for the Krell products (#8188)
2018-05-21Rename Tpetra C wrappers for *gemm Fortran functions in Trilinos 12.12.1 (#8228)Dan FitzGerald2-2/+293
* Updated trilinos to compile/install with xl_r * Undo PGI patch added as part of Trilinos XL fix * Remove PGI related changes in Trilinos XL fix
2018-05-21Add Python/Ruby bindings to GEOS package (#8218)Adam J. Stewart1-20/+35
* Add python/ruby bindings to GEOS package * Add comment on Python 3 support
2018-05-21Add lcms 2.9 (#8219)Adam J. Stewart1-1/+3
2018-05-21Add missing dependencies to poppler package (#8220)Adam J. Stewart2-3/+162
2018-05-21Add bmake 20180512 (#8221)Adam J. Stewart1-16/+18
* Add bmake 20180512 * Re-add manpage patch
2018-05-21py-testinfra: Add versions 1.12.0 and 1.13.0 (#8222)Eric1-0/+2
2018-05-21Add info about haveged to gpg/randomness note (#8227)George Hartzell1-3/+18
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