Commit graph

4466 commits

Author SHA1 Message Date
scheibelp
6243a28da1 Don't change properties on already-installed packages (#5580)
* edits to address issues where spack concretization attempts to set properties on already-installed specs

* most added checks only need to check if the spec is concrete; they dont also need to check if the package is installed

* add test to ensure that patches are not applied to an installed spec

* add test to ensure that an error is detected when a dependent requests a dependency constraint which conflicts with a requested installed dependency
2017-10-05 10:33:04 -07:00
lingnanyuan
747b584e2e r-acme: Create new package. (#5620) 2017-10-05 10:22:24 -06:00
lingnanyuan
b41dfa8bd2 r-acgh: Create new package. (#5619) 2017-10-05 10:22:03 -06:00
lingnanyuan
a66eb716a7 r-cluster: Update version to 2.0.6. (#5618) 2017-10-05 10:21:44 -06:00
lingnanyuan
58609c5b67 r-absseq: Create new package. (#5617) 2017-10-05 10:21:33 -06:00
lingnanyuan
2c300653d5 r-acde: Create new package. (#5616) 2017-10-05 10:21:17 -06:00
lingnanyuan
4a1351c546 r-boot: Update version to 1.3-20 (#5615) 2017-10-05 10:20:45 -06:00
Michael Kuhn
fe551a4d9a esmf: Fix build (#5607)
- Use libs instead of lapack_libs (see #3364).
- Add a patch to fix building with recent versions of gcc.
- Add a patch to fix building with mvapich2.
2017-10-05 08:58:40 -06:00
lingnanyuan
21c79edb10 r-abadata: new package. (#5611) 2017-10-05 08:58:04 -06:00
lingnanyuan
f54e30b065 r-abaenrichment: Create new package. (#5612) 2017-10-05 08:57:42 -06:00
Axel Huebl
44653dc7aa CMake: 3.9.4 (#5614)
Adds the latest release of CMake.
2017-10-05 08:57:20 -06:00
Christoph Junghans
ffe90834b3 Add the Sandbox package (#5595) 2017-10-04 18:40:03 -07:00
Ben Boeckel
44fbf95dd4 extensions: create install prefixes (#5601)
Tests fail locally because the install prefix doesn't exist. Make them
exist.
2017-10-04 14:08:05 -07:00
Yifan Zhu
2b7a37ed99 r-tibble: added dependency r-rlang (#5536)
* pr-quantities: add version & py-numpy conflict (#5307)

* r-tibble: Update version to 1.3.4

* r-tibble: added dependency r-rlang

* r-tibble: changed r-lazyeval and r-rlang to be versioned dependencies

* Update package.py

* Update package.py
2017-10-04 09:59:40 -07:00
Audrey Thoma
727e542b80 tassel: new package (#5583) 2017-10-04 10:28:28 -06:00
Michael Kuhn
1d8b77b600 xerces-c: Fix url (#5597)
The main location only carries the latest release, while all previous
(and current) ones are available at the archive location.
2017-10-04 10:25:31 -06:00
Axel Huebl
a8bf49b4a1 OpenSSL: Fix Zlib (#5584)
Fix missing `-lz` on `make` of OpenSSL.
Spotted on a system without a system-wide zlib installation.
2017-10-04 10:25:11 -06:00
Yifan Zhu
ed656dccf5 r-edger: created new package (#5571) 2017-10-03 17:34:46 -06:00
George Hartzell
23454e3e28 Add package for multitail@6.4.2 (#5567)
* Add package for multitail@6.4.2

Lightly tested on CentOS 7.

* Responde to feedback/comments

Use `install_targets` to specify PREFIX= and DESTDIR= instead of
hacking away at the Makefile.  Expand commentary about "Why?".

Use `headers.include_flags` and `libs.ld_flags` to avoid explicitly
setting `-L` and `-I` when hacking away at the Makefile.
2017-10-03 16:05:19 -06:00
Robert Pavel
9871a2eb91 ExaSP2 Spackage (#5570)
* Added exasp2 spackage

Added spackage for exasp2 proxy app

* Fixed MPI in ExaSP2

Explicitly disabled MPI when not enabled.
Set MPI variant to default as per Spack standards

* Generalized BML Passing for ExaSP2

* Modified to follow spack rules on blas

Fortunately was able to modify exasp2 build system to support spack
model for blas and lapack requirements. No guarantee is made for support
of anything other than originally supported libraries

* Fixed flake8 error
2017-10-03 16:04:49 -06:00
lingnanyuan
a05964959d r-a4base: new package. (#5576) 2017-10-03 16:04:18 -06:00
lingnanyuan
e858e4de17 r-a4: new package. (#5577) 2017-10-03 16:03:57 -06:00
Audrey Thoma
0fa3d8f35e fastqvalidator: new package (#5573)
* fastqvalidator: new package

* adding version-specificity to compiler conflict

* quick changes to env vars and build phase

* Update package.py

* oops. forgot to install executable

* Update package.py

* updating package.py

* turn env into targets
2017-10-03 15:56:32 -06:00
Axel Huebl
ba06eb72d0 libpng: zlib path (#5581)
explicitly set the zlib path for libpng configure.

fixes:
```
     [ ... ]
     92    checking for memset... yes
     93    checking for pow... no
     94    checking for pow in -lm... yes
     95    checking for clock_gettime... yes
     96    checking for zlibVersion in -lz... no
     97    checking for z_zlibVersion in -lz... no
  >> 98    configure: error: zlib not installed
```
2017-10-03 14:58:28 -06:00
Audrey Thoma
3e79872ada sra-toolkit: new package (#5588)
* sra-toolkit: new package

* adding description and homepage
2017-10-03 14:41:41 -06:00
George Hartzell
5bc81c8db2 Tell configure about gmp (#5585)
This is a partial fix for #5564.

This package used to trust that `configure` would discover `gmp` from
its environment.

It's safer to tell it where to find `gmp` explicitly.

This does that by adding a configure_args() that provides a
`--with-gmp=...` argument for configure.
2017-10-03 14:40:14 -06:00
Audrey Thoma
35085fdae2 mrtrix3: new package (#5568)
* mrtrix3: new package

* specifying conflict dependency ve
2017-10-02 15:56:15 -06:00
lingnanyuan
140fbeda65 r-a4reporting: new package. (#5575) 2017-10-02 15:54:44 -06:00
Yifan Zhu
960dcec9e3 r-locfit: created new package (#5572) 2017-10-02 15:54:26 -06:00
Robert Pavel
d3e4e88bae Added support for BML+mpi variant (#5563)
* Added support for BML+mpi variant

Added support for BML+mpi variant. Currently restricted to master
(develop) branch pending release of next bml tag

* Update package.py

Removing redundant statement

* Update package.py

Added explicit disabling of MPI when not requested
2017-10-02 12:51:06 -06:00
Robert Pavel
0d0d2663d2 Added Spackage for YAJL (#5566)
Added spackage for YAJL
2017-10-02 12:50:55 -06:00
Audrey Thoma
538b702314 linkphase3: new package (#5493)
* linkphase3: new package

* adding ifort option

* Update package.py
2017-10-02 12:36:39 -06:00
Audrey Thoma
7cb2766790 hisat2: new package (#5488) 2017-10-02 10:27:06 -07:00
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