Commit graph

4433 commits

Author SHA1 Message Date
Axel Huebl
48e4efc2a4 CUDA 9.0.176 (#5562)
The first stable release of CUDA 9, v9.0.176, is out.

This adds its installer and checksum.
2017-10-02 10:47:32 -06:00
Todd Gamblin
4f8c7d57eb Patches are hashed with specs, and can be associated with dependencies.
- A package can depend on a special patched version of its dependencies.

  - The `Spec` YAML (and therefore the hash) now includes the sha256 of
    the patch in the `Spec` YAML, which changes its hash.

  - The special patched version will be built separately from a "vanilla"
    version of the same package.

  - This allows packages to maintain patches on their dependencies
    without affecting either the dependency package or its dependents.
    This could previously be accomplished with special variants, but
    having to add variants means the hash of the dependency changes
    frequently when it really doesn't need to.  This commit allows the
    hash to change *just* for dependencies that need patches.

  - Patching dependencies shouldn't be the common case, but some packages
    (qmcpack, hpctoolkit, openspeedshop) do this kind of thing and it
    makes the code structure mirror maintenance responsibilities.

- Note that this commit means that adding or changing a patch on a
  package will change its hash.  This is probably what *should* happen,
  but we haven't done it so far.

  - Only applies to `patch()` directives; `package.py` files (and their
    `patch()` functions) are not hashed, but we'd like to do that in the
    future.

- The interface looks like this: `depends_on()` can optionally take a
  patch directive or a list of them:

     depends_on(<spec>,
                patches=patch(..., when=<cond>),
                when=<cond>)
     # or
     depends_on(<spec>,
                patches=[patch(..., when=<cond>),
                         patch(..., when=<cond>)],
                when=<cond>)

- Previously, the `patch()` directive only took an `md5` parameter.  Now
  it only takes a `sha256` parameter.  We restrict this because we want
  to be consistent about which hash is used in the `Spec`.

- A side effect of hashing patches is that *compressed* patches fetched
  from URLs now need *two* checksums: one for the downloaded archive and
  one for the content of the patch itself.  Patches fetched uncompressed
  only need a checksum for the patch.  Rationale:

  - we include the content of the *patch* in the spec hash, as that is
    the checksum we can do consistently for patches included in Spack's
    source and patches fetched remotely, both compressed and
    uncompressed.

  - we *still* need the patch of the downloaded archive, because we want
    to verify the download *before* handing it off to tar, unzip, or
    another decompressor.  Not doing so is a security risk and leaves
    users exposed to any arbitrary code execution vulnerabilities in
    compression tools.
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
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
Gregory Lee
16bd1449be added qt creator version 4.4.0 (#5518) 2017-09-27 21:49:33 -06:00
lingnanyuan
d5fcbab8de r-varselrf: new package. (#5515)
* pr-quantities: add version & py-numpy conflict (#5307)

* r-varselrf: Create new package.
2017-09-27 21:48:22 -06:00
lingnanyuan
97208d9888 r-pamr: new package (#5514)
* pr-quantities: add version & py-numpy conflict (#5307)

* r-pamr: Create new package.
2017-09-27 21:48:04 -06:00
lingnanyuan
51e99c5fde r-rocr: new package. (#5513)
* pr-quantities: add version & py-numpy conflict (#5307)

* r-rocr: Create new package.
2017-09-27 21:47:47 -06:00