lingnanyuan
3921948b03
r-statmod: Create new package. ( #6119 )
2017-11-03 14:20:14 -06:00
lingnanyuan
b204c7e793
r-deseq: Create new package. ( #6118 )
2017-11-03 14:19:38 -06:00
lingnanyuan
f91c25ddee
r-samr: Create new package. ( #6117 )
2017-11-03 14:19:16 -06:00
lingnanyuan
d54627659a
r-impute: Create new package. ( #6116 )
2017-11-03 14:18:46 -06:00
lingnanyuan
95e290eaf3
r-altcdfenvs: Create new package. ( #6115 )
2017-11-03 14:18:17 -06:00
lingnanyuan
64689bdb01
r-makecdfenv: Create new package. ( #6114 )
2017-11-03 14:17:58 -06:00
lingnanyuan
b614c7970b
r-hypergraph: Create new package. ( #6113 )
2017-11-03 14:17:36 -06:00
Johann Klähn
3fc8a71afb
Fix restaging of resources ( #5681 )
...
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.
2017-11-03 11:29:43 -07:00
Todd Gamblin
12f0725e9f
spack fetch: don't fetch externals. ( #6124 )
...
Fixes #6123
spack fetch shouldn't attempt to fetch external deps when invoked
with --dependencies.
2017-11-03 10:15:15 -07:00
Axel Huebl
5a4544ab05
ISAAC 1.3.2 ( #6129 )
...
Add a new release of ISAAC.
2017-11-03 14:58:38 +01:00
Michael Kuhn
bd7d61325f
Configure user for mock Git repository ( #6128 )
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If user.useConfigOnly is set globally and no name or e-mail is
configured, the git_fetch tests fail.
2017-11-02 21:43:28 -07:00
Ben Boeckel
0f896e921f
test_activations: also test perl activations
2017-11-02 18:45:40 -07:00
Peter Scheibel
3a2a0c9ad4
test_activations: test Python's extension logic
2017-11-02 18:45:40 -07:00
Peter Scheibel
dde93c01cf
spec: support a test prefix
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This is used in tests to test real packages without actually building
and installing them.
2017-11-02 18:45:40 -07:00
Ben Boeckel
be01b2d5f0
aspell: refuse to work with non-global extensions
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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.
2017-11-02 18:45:40 -07:00
Ben Boeckel
a81485cb3f
perl: support extensions in views
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
643a28aac5
python: extensions support for easy-install.pth
2017-11-02 18:45:40 -07:00
Ben Boeckel
d5a3d9d20e
view: test conflicting packages in views
2017-11-02 18:45:40 -07:00
Ben Boeckel
13b669de8e
view: test that extension paths exist
2017-11-02 18:45:40 -07:00
Ben Boeckel
a06c6b0366
filesystem_view: reject packages with activations
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If there are extensions that are globally activated, reject adding them
to a view. Those extensions should not be implicitly activated.
2017-11-02 18:45:40 -07:00
Ben Boeckel
26724688b1
view: test viewing external packages
2017-11-02 18:45:40 -07:00
Ben Boeckel
ea62347c46
view: add a test for extension activation
2017-11-02 18:45:40 -07:00
Ben Boeckel
41dfba0ba1
extension1: add a second version
2017-11-02 18:45:40 -07:00
Ben Boeckel
4511d9d924
extensions: support only showing a subset of information
2017-11-02 18:45:40 -07:00
Ben Boeckel
b7ec870c3b
extensions: support acting on a view
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This allows extensions to be (de)activated and queried within a view
rather than only acting on the global installation.
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
db529f5b61
view: use the FilesystemView abstraction for creating views
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
af42c24ef5
view: fix some docstrings for arguments
2017-11-02 18:45:40 -07:00
Ben Boeckel
9a39efd966
filesystem_view: do not link external packages
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
538d855e1b
filesystem_view: add a class to handle a view via a Yaml description
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
21dc31a4a1
package: support removing dependencies when deactivating
2017-11-02 18:45:40 -07:00
Ben Boeckel
f50ddeed9f
conftest: mock out spack.store.extensions as well
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
078f85a125
views: support querying view layouts as well
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This abstracts out the layout in use between the global installations
and a specific view.
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
00a893aa79
link_tree: support choosing the link function
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This can be used to make hardlinks rather than symlinks.
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
9024ddcf05
link_tree: support ignoring conflicts
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
20cd82dc56
directory_layout: add a YamlExtensionsLayout class
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This uses a view to query extensions.
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
94c0740a88
link_tree: only remove matching files when unmerging
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
b9e8402104
directory_layout: factor out an ExtensionsLayout class
2017-11-02 18:45:40 -07:00
Ben Boeckel
650ca7db9e
extensions: add an installed_extensions_for method
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
56bafdc282
database: rename installed_extensions_for
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Views support activating packages, so rename the method because it will
soon query what is activated versus what is installed.
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
70d3558596
package: support verbosity when activating
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
af0cf2d3c6
package: rename activated to is_activated
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This allows the activation code to be later given parameters.
2017-11-02 18:45:40 -07:00
Ben Boeckel
f31b47c353
cmd/test: fix a typo in a comment
2017-11-02 18:45:40 -07:00
Ben Boeckel
6f9bf197a5
spec_yaml: fix a typo
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
28cc077ef6
view: fix a typo
2017-11-02 18:45:40 -07:00
Ben Boeckel
76305038ef
determine full compiler version for gcc-7
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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'
2017-11-02 18:44:10 -07:00
Ben Boeckel
a7925bb927
bdftopcf: require xproto and fontsproto at build time ( #6112 )
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These are technically "link" depends of libxfont, but they have no
actual libraries.
Fixes #5936 .
2017-11-02 15:47:18 -06:00
lingnanyuan
13f1781bea
Add package r-reportingtools and update url for its dependencies. ( #6071 )
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* r-reportingtools: Create new package.
* r-go-db: Update url.
* r-gseabase: Update url.
* r-pfam-db: Update url.
2017-11-02 14:21:32 -06:00
Michael Kuhn
d1db161aeb
adios: Fix hdf5 and sz dependencies ( #6016 )
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- 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.
2017-11-02 13:41:25 -06:00
Brice Goglin
3a1b013291
hwloc: add version 1.11.8 ( #6099 )
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Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
2017-11-02 13:40:46 -06:00
Audrey Thoma
f9341857c7
arlecore: new package ( #6109 )
2017-11-02 13:40:03 -06:00
