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2018-12-17GDL: python integration fixes (#9936)Ricardo Silva2-5/+69
* GDL: python integration fixes * renamed python-related variants to follow the convention * building the Python module requires patches currently targetting 0.9.8 othwerwise asking for the Python module *only* builds the Pyhton module * building the python module also requires patching the vendored (with the GDL) antlr to be built as a shared library * Typo Co-Authored-By: rmsds <ricardo.d.silva@gmail.com> * Rename embed-python variant to embed_python
2018-12-17zoltan: rely on MPI wrappers instead of guessing MPI libraries (#8986)TZ1-25/+5
* zoltan: only add gussed MPI libs if no MPI wrappers are used - if MPI-wrappers are used for compilation, we can assume that linking works without manually specifying MPI libs (guessing may result in wrong libs, cf. #8979) - thus, only guess the NPI libs and add them explicitly if no MPI-wrappers are used - use llnl.util.filesystem.find_libraries instead of a locally defined routine to guess the MPI libs if needed (cf. #8979) * zoltan: rely on MPI-wrappers to know the required MPI libs
2018-12-17mark: Create new package. (#7069)lingnanyuan1-0/+53
* mark: Create new package. * mark: change description. * mark: change description. * mark: Delete set_up environment. * mark: replace join_path(prefix.bin, mark) with prefix.bin.mark
2018-12-17Add latest version of atk (#10125)Adam J. Stewart1-3/+6
2018-12-16packages/phist: new version 1.7.5 (#10120)jthies1-0/+1
2018-12-15r-multitaper: new package at 1.0-14 (#10110)Justin Stanley1-0/+18
2018-12-15r-popgenome: new package at 2.6.1 (#10108)Justin Stanley1-0/+21
2018-12-15r-xnomial: new package at 1.0.4 (#10111)Justin Stanley1-0/+21
* r-xnomial: new package at 1.0.4 * r-xnomial: add list_url
2018-12-14Add latest version of libsigcpp (#10103)Adam J. Stewart1-1/+7
2018-12-14Add latest version of bdw-gc (#10100)Adam J. Stewart1-2/+4
2018-12-14Add latest version of libatomic-ops (#10099)Adam J. Stewart1-2/+3
2018-12-14pbsuite: pythonpath should be prepended not set (#10113)Levi Baber1-1/+1
2018-12-14clp: add explicit datadir (#10109)Justin Stanley1-0/+5
2018-12-14Updates to Google Test: (#10079)Andrew Gaspar1-3/+4
- Add version 1.8.1 - Change to sha256 checksums
2018-12-14qt: fix openssl dependency for older versions (#10106)Michael Kuhn1-0/+1
2018-12-14Add latest version of libxslt (#10098)Adam J. Stewart1-8/+8
2018-12-14Add latest version of poppler (#10101)Adam J. Stewart1-1/+2
2018-12-14Add latest version of cairo (#10102)Adam J. Stewart1-1/+3
2018-12-14Fix spack package inheritance for module variables (#10097)Greg Becker2-0/+26
* we weren't properly setting module variables for the root package in a DAG -- just for transitive dependencies.
2018-12-14Add latest version of meson (#10104)Adam J. Stewart1-2/+4
2018-12-14make dtcmp an autotools spackage (#10095)Elsa Gonsiorowski, PhD1-6/+3
* make dtcmp an autotools spackage * better code
2018-12-13Add new packages for ELSD and ELSDc (#10072)Adam J. Stewart2-0/+56
2018-12-13cmake: add version 3.13.2 (#10092)Matthias Diener1-0/+1
2018-12-13Feature/spm (#10053)Miles Perry1-0/+32
* extract spm12.ctf to get binaries and libraries * flake8 edits * flake8 edits * spm: updates * spm: previous version
2018-12-13trf: add version 4.07b and install fixes (#10093)Eric1-2/+8
* trf: add version 4.07 and install fixes * suggested fixes
2018-12-13superlu-dist: update v6.1.0 checksum (#10078)Satish Balay1-1/+1
2018-12-13Add CUDA_HOME variable to cuda module file. (#10088)Jon Rood1-0/+3
2018-12-12lammps: add new stable version (#10086)Christoph Junghans1-0/+3
2018-12-12boost: add 1.69.0 (#10083)Denis Davydov1-0/+3
signals (v1) was removed in 1.69.0
2018-12-11LEMON: Create new package (#10077)Eric1-0/+18
2018-12-11added sha256 for scr v1.2.0-2 (#10082)Elsa Gonsiorowski, PhD1-1/+3
2018-12-11gcc: fix sys_ustat.h patch for gcc 4.8 and 4.9 (#10081)Mark W. Krentel2-1/+36
The sys_ustat.h.patch to file sanitizer_platform_limits_posix.cc from PR #10046 does not apply cleanly to gcc 4.8 or 4.9 (or earlier). GCC up to 4.8.x either don't have libsanitizer or else don't include ustat.h in sanitizer_platform_limits_posix.cc. GCC 4.9.x includes ustat.h, but needs a slightly different patch. The patch applies to GCC 5.x up to 6.4, and 7.x up to 7.3 and also 8.1.0. The patch is already included in the tar files for gcc 6.5.0, 7.4.0 and 8.2.0.
2018-12-11flux-core & flux-sched: fix compilation and dependencies (#10049)Stephen Herbein2-3/+12
* flux-sched: fix compilation errors configure was being run twice becuase the staging symlinks were confusing autotools mirror flux-core in building in a subdirectory to avoid other common compilation problems, like the one in PR #3543 * flux-core: update dependencies munge is no longer a dependency provide hints for lua version so that `spack install flux-core` works "out-of-the-box". Currently, when no explicity version is provided, the concretizer attempts to use lua@5.3, which is invalid. Closes #10000
2018-12-10Update LBANN generator and bug fix (#9906)Brian Van Essen3-13/+28
* Added a package for the MDAnalysis toolkit. * Added Ninja as the generator for LBANN, Hydrogen, and Aluminum. Also fixed a bug in how the Conduit variant is included in LBANN. Added new versions for Hydrogen and LBANN. * Updated lbann package so that the CMAKE parameters are set when the variant is on and off.
2018-12-10mofem: add new releases and minor changes (#9138)Lukasz5-48/+79
2018-12-10cloc: URLs are now consistent (#10068)Matthias Diener1-3/+1
Fixed in upstream: https://github.com/AlDanial/cloc/issues/352
2018-12-09metis: Fix issues with gcc6 and misleading indentation (#10058)Tom Payerle2-0/+13
Added patch to GKlibSystem.cmake to disable warnings (which get promoted to errors) due to -Wmisleading-indentation being added to -Wall in gcc 6
2018-12-08gcc: add versions 7.4, 6.5 (#10061)Matthias Diener1-0/+6
2018-12-08OpenMPI: adding static libraries with slurm support for latest versions. ↵Jon Rood1-0/+4
(#10055)
2018-12-08TraceR: add release tag/version (#10054)Abhinav Bhatele1-0/+1
2018-12-08pumi: shared variant (#10057)Cameron Smith1-0/+2
2018-12-08eztrace: add new package (#10060)Matthias Diener1-0/+25
2018-12-07r-expint: new package at 0.1-5 (#10043)Justin Stanley1-0/+19
2018-12-07Fix Catch2 Single Header (#10022)Axel Huebl1-1/+4
Fix the install of the single header amalgate in catch2. The public API for catch < 2.3.0 was "#include <catch.hpp>". For 2.3.0+ it is "#include <catch2/catch.hpp>"
2018-12-07gcc: Add patch to build GCC with glibc 2.28 and later (#10046)James Clark2-0/+65
2018-12-07pbsuite: new package at 15.8.24 (#10059)Justin Stanley1-0/+28
2018-12-07scallop: new package at 0.10.3 (#10041)Justin Stanley1-0/+26
2018-12-07r-sseq: new package at 1.20.0 (#10042)Justin Stanley1-0/+20
2018-12-07r-blockmodeling: new package at 0.3.1 (#10044)Justin Stanley1-0/+22
2018-12-07Spades: Add version 3.13.0 (#10033)Mario Melara1-1/+2
* Spades: Add version 3.13.0 In version 3.13.0 the CmakeLists.txt dir is at a different location than in other versions. Versions up to 3.12.0 are located in "src" whereas 3.13.0 is a level deeper at "assemblers/src". * Remove git and add new version hash
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