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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
2017-11-02filesystem_view: do not link external packagesBen Boeckel1-0/+10
2017-11-02filesystem_view: add a class to handle a view via a Yaml descriptionOliver Breitwieser1-0/+524
2017-11-02package: support removing dependencies when deactivatingOliver Breitwieser1-6/+14
2017-11-02conftest: mock out spack.store.extensions as wellBen Boeckel1-0/+4
2017-11-02views: support querying view layouts as wellOliver Breitwieser5-26/+56
This abstracts out the layout in use between the global installations and a specific view.
2017-11-02link_tree: support choosing the link functionOliver Breitwieser1-2/+2
This can be used to make hardlinks rather than symlinks.
2017-11-02link_tree: support ignoring conflictsOliver Breitwieser1-3/+16
2017-11-02directory_layout: add a YamlExtensionsLayout classOliver Breitwieser1-0/+25
This uses a view to query extensions.
2017-11-02link_tree: only remove matching files when unmergingOliver Breitwieser1-1/+6
2017-11-02directory_layout: factor out an ExtensionsLayout classOliver Breitwieser1-92/+118
2017-11-02extensions: add an installed_extensions_for methodBen Boeckel2-1/+11
2017-11-02database: rename `installed_extensions_for`Oliver Breitwieser3-3/+3
Views support activating packages, so rename the method because it will soon query what is activated versus what is installed.
2017-11-02package: support verbosity when activatingOliver Breitwieser1-8/+14
2017-11-02package: rename `activated` to `is_activated`Oliver Breitwieser4-10/+10
This allows the activation code to be later given parameters.
2017-11-02cmd/test: fix a typo in a commentBen Boeckel1-1/+1
2017-11-02spec_yaml: fix a typoBen Boeckel1-1/+1
2017-11-02view: fix a typoOliver Breitwieser1-1/+1
2017-11-02determine full compiler version for gcc-7Ben Boeckel1-1/+4
Fixes #5778. Spack uses 'gcc -dumpversion' to determine the full version of gcc. 'gcc -dumpversion' no longer gives the full version on gcc 7.2.0. 'gcc -dumpfullversion' is required instead. This PR detects when 'gcc -dumpversion' gives a truncated version of '7' and in that case retrieves the full version with 'gcc -dumpfullversion'
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.