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2017-11-06repeatmasker: new package (#6108)Audrey Thoma3-0/+162
2017-11-06Introduce static_to_shared_library function (#6092)Michael Kuhn2-73/+4
The static_to_shared_library function takes an existing static library and produces a shared library based on it.
2017-11-06trilinos: update hdf5 dependency to use 'hdf5+hl' (#6025)Satish Balay1-1/+2
* trilinos: update hdf5 dependency to use 'hdf5+hl' Without this change - I get the following error [triggered by 161dca6d5 c9810f808 changes] $ ./bin/spack install trilinos+hdf5 ==> Error: An unsatisfiable variant constraint has been detected for spec: hdf5@1.10.1%gcc@7~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-fedora27-x86_64 while trying to concretize the partial spec: netcdf+mpi ^m4 ^mpich@3.3a2%gcc@7 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-fedora27-x86_64 ^zlib@1.2.11%gcc@7+optimize+pic+shared arch=linux-fedora27-x86_64 netcdf requires hdf5 variant +hl, but spec asked for ~hl * fix flake8 warning
2017-11-06some missing X11 "*proto" dependencies (#6158)Luigi Calori4-0/+8
* fix xinput deps * adding other x11 proto missing deps, see #6157
2017-11-06petsc: update petsc dependency on superlu-dist (#6159)Satish Balay1-2/+4
2017-11-06Bioconductor package url change (#5797)Yifan Zhu21-52/+54
2017-11-06likwid: Use external lua if possible (#6009)Michael Kuhn1-2/+18
2017-11-06added new package - MotionCor2 (#6151)Douglas Duckworth1-0/+50
2017-11-06dealii: make sure bundled libs are not used (#6106)Denis Davydov1-1/+2
2017-11-05Graphviz : Add a GTS variant (#6149)Besnard Jean-Baptiste1-1/+5
Enable support for the GNU Triangulated Surface Library - New variant +gts for graphviz - Optionnal dependency for GTS (already packaged)
2017-11-05added relion v 2.1 (#6023)Douglas Duckworth1-3/+3
* added relion v 2.1 * relion 2.1 - misssed comma * relion now pulling from master branch - removed 2.03 - added cuda 8 as dependency given 9 does not yet work with relion per https://github.com/3dem/relion/issues/296
2017-11-05Re-add list_url for all R packages (#6110)Ben Boeckel245-50/+245
* r-igraph: find old packages in the archive Fixes #6104. * r-irlba: find old packages in the archive Fixes #6101. * r-lazyeval: find old packages in the archive Fixes #6102. * packages: set list_url for all packages hosted on CRAN * packages: consistently use the CRAN archive URLs
2017-11-05dtcmp: add v1.1.0 (#6146)Adam Moody1-0/+1
2017-11-05petsc: update to version 3.8.1 (#6150)Satish Balay1-0/+4
* petsc: update to version 3.8.1 * petsc: add in conflict between petsc-3.8.0 & mkl
2017-11-05ISAAC 1.3.3 (#6152)Axel Huebl1-0/+1
Add a new release of ISAAC.
2017-11-04Replace github.com/llnl/spack with github.com/spack/spack (#6142)Todd Gamblin2202-2227/+2227
We moved to a new GitHub org! Now make the code and docs reflect that.
2017-11-04add rol variant (#6105)vishalkenchan1-0/+4
2017-11-03r-yapsa: created new package (#6121)Yifan Zhu1-0/+57
2017-11-03r-keggrest: created new package (#6120)Yifan Zhu1-0/+44
2017-11-03r-statmod: Create new package. (#6119)lingnanyuan1-0/+42
2017-11-03r-deseq: Create new package. (#6118)lingnanyuan1-0/+46
2017-11-03r-samr: Create new package. (#6117)lingnanyuan1-0/+37
2017-11-03r-impute: Create new package. (#6116)lingnanyuan1-0/+36
2017-11-03r-altcdfenvs: Create new package. (#6115)lingnanyuan1-0/+43
2017-11-03r-makecdfenv: Create new package. (#6114)lingnanyuan1-0/+44
2017-11-03r-hypergraph: Create new package. (#6113)lingnanyuan1-0/+38
2017-11-03ISAAC 1.3.2 (#6129)Axel Huebl2-3/+6
Add a new release of ISAAC.
2017-11-02aspell: refuse to work with non-global extensionsBen Boeckel1-1/+13
Aspell compiles in the paths it looks for rather than looking relative to its binary location. There are also no environment variables to redirect it other than changing the path to the configuration file it looks at.
2017-11-02perl: support extensions in viewsBen Boeckel1-2/+8
2017-11-02python: extensions support for easy-install.pthOliver Breitwieser1-10/+30
2017-11-02view: test conflicting packages in viewsBen Boeckel2-4/+4
2017-11-02view: test that extension paths existBen Boeckel2-0/+6
2017-11-02extension1: add a second versionBen Boeckel1-0/+1
2017-11-02bdftopcf: require xproto and fontsproto at build time (#6112)Ben Boeckel1-0/+2
These are technically "link" depends of libxfont, but they have no actual libraries. Fixes #5936.
2017-11-02Add package r-reportingtools and update url for its dependencies. (#6071)lingnanyuan4-5/+71
* r-reportingtools: Create new package. * r-go-db: Update url. * r-gseabase: Update url. * r-pfam-db: Update url.
2017-11-02adios: Fix hdf5 and sz dependencies (#6016)Michael Kuhn1-2/+2
- hdf5's +hl variant is required because the build uses libhdf5_hl. - sz is only compatible up to version 1.4.10 because the library has been renamed to libSZ in 1.4.11.
2017-11-02hwloc: add version 1.11.8 (#6099)Brice Goglin1-0/+1
Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
2017-11-02arlecore: new package (#6109)Audrey Thoma1-0/+40
2017-11-02gromacs: add develop version (#6098)Christoph Junghans1-0/+1
2017-11-02sundials+hypre depends on hypre (#6075)Adam J. Stewart1-0/+2
2017-11-02the-silver-searcher: add missing dependency (#6095)Denis Davydov1-0/+1
2017-11-02xqilla: Use append instead of extend (#6094)Michael Kuhn1-1/+1
2017-11-01Update candle (#6097)Brian Van Essen1-0/+10
2017-11-01r-getoptlong: created new package (#6069)Yifan Zhu1-0/+42
2017-11-01r-gtrellis: created new package (#6088)Yifan Zhu1-0/+46
2017-11-01LBANN flags and OpenCV variant (#5951)Brian Van Essen3-13/+39
* Fixed the datatype flag in the LBANN package. Fixed where the datatype flag should be set. * Added variant to OpenCV to disable building DNN support * Fixed a bug in how the elemental package tries to find its Fortran library. The current method does not work with Intel compilers. * Added necessary paths for cuDNN and CUB. * Addressed flake8 issues in Elemental package. * Fixed several flake8 errors. Added variant to build with or without support for arbitrary-precision floating point arithmetic. * Added the proper CMake flag when MPFR support is disabled. * Fixed a bug in how the cudnn path was being set when there was no cudnn requested. Also requested that OpenCV is built without eigen support. * Fixed another bug where a dependency may not be there and thus should not be always checked.
2017-11-01lua: Build a shared library (#6008)Michael Kuhn2-0/+77
Patch is inspired by Arch Linux and Homebrew.
2017-11-01r-circlize: new package (#6087)Yifan Zhu1-0/+48
2017-11-01r-alsace: Create new package. (#6064)lingnanyuan1-0/+43
2017-11-01r-globaloptions: new package (#6068)Yifan Zhu1-0/+40