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2017-11-06add artisanal handcrafted SVG Spack logo. (#6165)Todd Gamblin10-3/+384
- This isn't one of those autogenerated SVGs from a drawing program! - This is a completely re-traced, minimalist SVG file with clearly delineated pieces so that your favorite renderer can draw a Spack logo at whatever resolution you want. - Included versions with text, as well.
2017-11-06Fix spack view hardlink (#6130)Johann Klähn2-1/+14
Fix a typo in "spack view hardlink" introduced in #5415 ("os.hardlink" does not exist).
2017-11-06repeatmasker: new package (#6108)Audrey Thoma3-0/+162
2017-11-06Introduce static_to_shared_library function (#6092)Michael Kuhn4-73/+201
The static_to_shared_library function takes an existing static library and produces a shared library based on it.
2017-11-06Docs: MPI as Root (#6156)Axel Huebl1-0/+3
New versions of OpenMPI need `--allow-run-as-root` for running as root: http://www.open-mpi.de/doc/v2.0/man1/mpirun.1.php#toc22
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
2017-11-06Add back help placeholder for "spack load" (#6127)scheibelp5-8/+30
Fixes #6126 #3183 removed the print_help function from the "modules" module. This adds it back so that if a user invokes 'spack load foo' without having sourced an environment setup script, they will be prompted to do so. This also improves the placeholder message to tell the user to invoke 'spack' as shell function rather than as an executable.
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 Gamblin2488-2542/+2542
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
2017-11-03Fix restaging of resources (#5681)Johann Klähn1-12/+22
Part of the resource staging process is to place downloaded/expanded files in the root stage. This was not happening when a resource stage was restaged.
2017-11-03spack fetch: don't fetch externals. (#6124)Todd Gamblin1-1/+8
Fixes #6123 spack fetch shouldn't attempt to fetch external deps when invoked with --dependencies.
2017-11-03ISAAC 1.3.2 (#6129)Axel Huebl2-3/+6
Add a new release of ISAAC.
2017-11-02Configure user for mock Git repository (#6128)Michael Kuhn1-0/+2
If user.useConfigOnly is set globally and no name or e-mail is configured, the git_fetch tests fail.
2017-11-02test_activations: also test perl activationsBen Boeckel1-0/+103
2017-11-02test_activations: test Python's extension logicPeter Scheibel1-0/+168
2017-11-02spec: support a test prefixPeter Scheibel1-0/+5
This is used in tests to test real packages without actually building and installing them.
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 Boeckel3-4/+29
2017-11-02view: test that extension paths existBen Boeckel3-0/+29
2017-11-02filesystem_view: reject packages with activationsBen Boeckel3-11/+26
If there are extensions that are globally activated, reject adding them to a view. Those extensions should not be implicitly activated.
2017-11-02view: test viewing external packagesBen Boeckel1-0/+9
2017-11-02view: add a test for extension activationBen Boeckel1-0/+82
2017-11-02extension1: add a second versionBen Boeckel1-0/+1
2017-11-02extensions: support only showing a subset of informationBen Boeckel1-32/+60
2017-11-02extensions: support acting on a viewBen Boeckel3-12/+40
This allows extensions to be (de)activated and queried within a view rather than only acting on the global installation.
2017-11-02view: use the FilesystemView abstraction for creating viewsOliver Breitwieser1-198/+127
2017-11-02view: fix some docstrings for argumentsOliver Breitwieser1-2/+2