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Author SHA1 Message Date
Todd Gamblin
94d85d842c Consolidate some web-spidering commands in spack.util.web 
- move `spack.cmd.checksum.get_checksums` to `spack.util.web.spider_checksums`

- move `spack.error.NoNetworkError` to `spack.util.web.NoNetworkError` since
  it is only used there.
 2017-09-30 02:06:59 -07:00
Todd Gamblin
2198a0e229 Disable duplicate cross-reference warnings in Sphinx. 2017-09-30 02:06:59 -07:00
Todd Gamblin
0e8bb9ec5e Refactor Package dependency metadata 
- Previously, dependencies and dependency_types were stored as separate
  dicts on Package.
  - This means a package can only depend on another in one specific way,
    which is usually but not always true.
  - Prior code unioned dependency types statically across dependencies on
    the same package.

- New code stores dependency relationships as their own object, with a
  spec constraint and a set of dependency types per relationship.
  - Dependency types are now more precise
  - There is now room to add more information to dependency relationships.

- New Dependency class lives in dependency.py, along with deptype
  definitions that used to live in spack.spec.

Move deptype definitions to spack.dependency
 2017-09-30 02:06:59 -07:00
Todd Gamblin
a3cb6b61ea Patch.apply() shouldn't affect working directory of caller. 2017-09-30 02:06:59 -07:00
Todd Gamblin
29ce69f3ed Only print "no patches needed" if there were no patches. 2017-09-30 02:06:59 -07:00
scheibelp
9e7faff6c9 Add test deptype (#5132) 
* Add '--test=all' and '--test=root' options to test either the root or the root and all dependencies.
* add a test dependency type that is only used when --test is enabled.
* test dependencies are not added to the spec, but they are provided in the test environment.
 2017-09-29 22:08:15 -07:00
Yifan Zhu
3c0e799a51 r-limma: added version 3.32.7 (#5558) 2017-09-29 16:29:41 -06:00
Jon Rood
ebbdde9625 Masa requires python if +python. (#5547) 2017-09-29 16:14:12 -06:00
lingnanyuan
756fb83f04 r-a4classif: new package. (#5557) 2017-09-29 16:06:27 -06:00
lingnanyuan
17b8f6b818 r-yaml: Correct url (#5550) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-yaml: Correct url.
 2017-09-29 16:05:55 -06:00
Yifan Zhu
7c87cb1ad1 r-downloader: created new package (#5556) 2017-09-29 16:05:30 -06:00
lingnanyuan
f9e33e9b59 r-mlinterfaces: new package. (#5555) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-mlinterfaces: Create new package.
 2017-09-29 15:34:44 -06:00
Yifan Zhu
06a6c6a399 r-biomart: created new package (#5554) 2017-09-29 15:33:40 -06:00
lingnanyuan
18029f5f47 r-threejs: Correct url. (#5553) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-threejs: Correct url.
 2017-09-29 15:33:05 -06:00
Jon Rood
d19eb152c8 Adding new Trilinos version and updating Nalu to utilize it. (#5552) 2017-09-29 15:31:15 -06:00
lingnanyuan
e1f33bd903 r-hwriter: new package. (#5549) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-hwriter: Create new package.
 2017-09-29 15:29:26 -06:00
lingnanyuan
211f731065 r-gbm: new package. (#5548) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-gbm: Create new package.
 2017-09-29 15:29:11 -06:00
lingnanyuan
4cc1ff5ce8 r-htmlwidgets: Update version to 0.8. (#5551) 2017-09-29 14:28:48 -07:00
lingnanyuan
89b30bea7f r-a4preproc: Create new package. (#5499) 2017-09-29 15:27:20 -06:00
Massimiliano Culpo
554937780b modules: specialized configure_options for external packages (#5543) 
closes #5473

Prior to this PR we were not exiting early for external packages, which
caused the `configure_options` property of the contexts to fail with
e.g. a key error because the DAG gets truncated for them. More
importantly Spack configure options don't make any sense for externals.

Now we exit early, and leave a message in the module file clarifying
that this package has been installed outside of Spack.
 2017-09-29 09:23:13 -07:00
Yifan Zhu
a63fdc8f35 r-dbi: updated to version 0.7 (#5537) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-dbi: Create new package.

* r-dbi: modified according to flake8

* Update package.py

* Update package.py
 2017-09-28 22:14:56 -06:00
lingnanyuan
aab68aaecf r-gdata: Update version to 2.18.0 (#5495) 2017-09-28 18:13:06 -07:00
Mark C. Miller
e851d15974 fixing tag name for development branch (#5496) 2017-09-28 18:12:02 -07:00
Yifan Zhu
aee44efada r-biostrings: created new package (#5498) 2017-09-28 18:11:28 -07:00
Yifan Zhu
b455fa2a7b r-gcrma: created new package (#5500) 2017-09-28 18:11:02 -07:00
Yifan Zhu
e42fd90df2 r-yaqcaffy: created new package (#5538) 2017-09-28 18:02:58 -07:00
Jon Rood
5e3024368e Add metaphysicl package (#5539) 
* Adding package Metaphysicl.

* Removing list_url from metaphysical package.
 2017-09-28 18:02:07 -07:00
Jon Rood
90e4b56362 Adding masa package. (#5541) 2017-09-28 18:01:38 -07:00
Yifan Zhu
6d63be9eb6 r-rlang: created new package (#5535) 2017-09-28 16:07:13 -06:00
Christoph Junghans
337256ee32 tycho2: initial commit (#5196) 2017-09-28 14:48:54 -07:00
Mark Olesen
aff6148116 Restrict openfoam to using openmpi+thread_multiple (partially resolves #5428) (#5479) 
- latest version requires openmpi+thread_multiple for collated output.
 2017-09-28 14:42:14 -06:00
Michael Kuhn
97bc86d617 snappy: Build shared library by default (#5534) 2017-09-28 14:18:50 -06:00
lingnanyuan
aa40509fa0 r-ggvis: Update version to 0.4.3 (#5532) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-ggvis: Update version to 0.4.3

* Update package.py

* Update package.py
 2017-09-28 13:13:47 -06:00
lingnanyuan
0962088776 r-dplyr: Update version to 0.7.3 (#5531) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-dplyr: Update version to 0.7.3

* Update package.py

* Update package.py
 2017-09-28 13:09:30 -06:00
Michael Kuhn
ac98e0978a ncl: Add tcsh dependency (#5195) 
All ncl scripts hardcode /bin/csh, so fix them up.
 2017-09-28 12:51:04 -06:00
Michael Kuhn
17be89c210 tcsh: New package (#5194) 
The patches are taken from the Fedora package.
 2017-09-28 12:50:52 -06:00
lingnanyuan
0bc3578dac r-annaffy: new package. (#5414) 
* r-annaffy: Create New Package.

* r-annaffy: Create new package.

* r-go-db: Create new package.

* r-kegg-db: Create new package.

* r-annaffy: Correct indentation.

* r-go-db: Correct indentation.

* r-kegg-db: Correct format.

* r-kegg-db: Correct format.

* r-go-db: Correct format.

* r-annaffy: Correct format.
 2017-09-28 12:49:31 -06:00
Audrey Thoma
3f44eb0179 fastq-screen: new package (#5431) 
* fastq-screen: new package

* fixing descriptions and previously made packages' old copyright date

* added wrong perl package after change
 2017-09-28 12:48:31 -06:00
Brian Homerding
0ce93d7333 Added hacckernels package (#5533) 2017-09-28 12:46:26 -06:00
lingnanyuan
d61e92b439 r-r6: Update version to 2.2.2 (#5529) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-r6: Update version to 2.2.2
 2017-09-28 12:46:11 -06:00
lingnanyuan
c0e1b1f68e r-shiny: update version to 1.0.5 (#5530) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-shiny: Update version to 1.0.5
 2017-09-28 11:31:27 -06:00
lingnanyuan
a613244602 r-htmltools: Update version to 0.3.6 (#5528) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-htmltools: Update version to 0.3.6
 2017-09-28 11:31:16 -06:00
lingnanyuan
0c385e94e6 r-httpuv: Update version to 1.3.5 (#5527) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-httpuv: Update version to 1.3.5
 2017-09-28 11:30:57 -06:00
lingnanyuan
38ea408126 r-rcpp: Update version to 0.12.13 (#5526) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-rcpp: Update version to 0.12.13

* r-rcpp: Correct url.
 2017-09-28 11:30:25 -06:00
Kelly (KT) Thompson
4e4247dd18 Provide a new Perl package 'cloc'. (#5525) 
+ Count, or compute differences of, physical lines of source code in the
  given files (may be archives such as compressed tarballs or zip files)
  and/or recursively below the given directories.
 2017-09-28 11:30:08 -06:00
lingnanyuan
e101665e5e r-jsonlite: Update version to 1.5 (#5524) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-jsonlite: Update version to 1.5
 2017-09-28 11:28:49 -06:00
lingnanyuan
4d445f8436 r-rda: new package. (#5523) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-rda: Create new package.
 2017-09-28 11:28:29 -06:00
Mark Olesen
cd825baee9 - build paraview without qt when osmesa is specified. (#5480) 
- new paraview version (5.4.1 from August)
 2017-09-27 22:32:10 -06:00
lingnanyuan
ab21d268be r-sfsmisc: new package. (#5516) 
* pr-quantities: add version & py-numpy conflict (#5307)

* r-sfsmisc: Create new package.

* r-sfsmisc: Correct format.
 2017-09-27 22:16:02 -06:00
Robert Pavel
b681146875 Added spackage for branson (#5520) 
Added spackage for branson proxy for monte carlo
 2017-09-27 21:50:07 -06:00