Commit graph

8321 commits

Author SHA1 Message Date
Ben Boeckel
a06c6b0366 filesystem_view: reject packages with activations
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
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
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
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
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
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
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
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)
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)
* 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)
- 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)
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
Todd Gamblin
c96f2e50a6
Only use XCode clang wrappers for packages that set use_xcode=True (#6077) 2017-11-02 09:19:23 -07:00
Christoph Junghans
c4db3d384e gromacs: add develop version (#6098) 2017-11-02 15:16:21 +01:00
Adam J. Stewart
e47ceefc43 sundials+hypre depends on hypre (#6075) 2017-11-02 08:16:43 +01:00
Denis Davydov
11ba60413b the-silver-searcher: add missing dependency (#6095) 2017-11-02 08:10:40 +01:00
Michael Kuhn
61ed583266 xqilla: Use append instead of extend (#6094) 2017-11-02 08:09:24 +01:00
Brian Van Essen
932068d725 Update candle (#6097) 2017-11-01 23:58:55 -06:00
scheibelp
3eb59f6932
update filename used for cc wrapper invocation debug log (#5837)
The name of the debug log written by the cc compiler wrapper was given
by Spec.short_spec, which includes the architecture. Somewhere along
the line Spec.format started adding spaces around the architecture
property so the filename started including spaces; the cc wrapper
script appears to ignore this, so files like spack-cc-bzip2-....in.log
(which record the wrapped compiler invocations) were not being
generated. This uses a different format string from the spec to
generate the wrapper log file names (which does not include spaces).
2017-11-01 20:11:00 -07:00
scheibelp
60a485591c Fix user specs which include already-installed packages (#5939)
* when a user-provided spec refers to an already-installed package, packages with patches applied were causing validation errors based on the recorded variants in the package's class

* avoid checks on all reserved variants (not just 'patches')
2017-11-01 18:44:31 -07:00
Yifan Zhu
7d0c6361ee r-getoptlong: created new package (#6069) 2017-11-01 19:09:54 -06:00
Yifan Zhu
f15969d624 r-gtrellis: created new package (#6088) 2017-11-01 19:09:20 -06:00
Brian Van Essen
86b7b84ddf LBANN flags and OpenCV variant (#5951)
* 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.
2017-11-01 17:25:28 -07:00
Michael Kuhn
0d624eac55 lua: Build a shared library (#6008)
Patch is inspired by Arch Linux and Homebrew.
2017-11-01 17:10:14 -06:00
Yifan Zhu
f3af8272f5 r-circlize: new package (#6087) 2017-11-01 17:08:46 -06:00
lingnanyuan
ef240f59b8 r-alsace: Create new package. (#6064) 2017-11-01 17:04:56 -06:00
Yifan Zhu
26ade0c9ae r-globaloptions: new package (#6068) 2017-11-01 17:04:38 -06:00
lingnanyuan
a05cca49d8 r-affycoretools: Create new package and its dependency r-ff. (#6082)
* r-ff: Create new package

* r-affycoretools: Create new package.

* r-ff: update url.
2017-11-01 17:04:17 -06:00
lingnanyuan
541818ed06 r-agimicrorna: Create new package. (#6083) 2017-11-01 17:03:48 -06:00
Yifan Zhu
616a43b76d r-complexheatmap: created new package (#6084) 2017-11-01 17:03:30 -06:00
Yifan Zhu
ebff5086d7 r-shape: created new package (#6086) 2017-11-01 17:03:15 -06:00