Commit graph

4602 commits

Author SHA1 Message Date
Yifan Zhu
4d3424a5d4 r-preprocesscore: added versioned dependency on r (#5671) 2017-10-13 18:50:26 -06:00
Yifan Zhu
e6109381fc r-rmpi: added list_url and updated md5 (#5698) 2017-10-13 18:35:06 -06:00
Yifan Zhu
ad8b9522d6 r-edger: added versioned dependency on r (#5669) 2017-10-13 18:32:43 -06:00
Yifan Zhu
8c2fe52f8e r-s4vectors: added versioned dependency on r (#5672) 2017-10-13 18:32:17 -06:00
Denis Davydov
c13e13a52b likwid: update versions (#5757) 2017-10-13 16:08:49 -06:00
Yifan Zhu
2c73c9fb50 r-xvector: added versioned dependency on r (#5731) 2017-10-13 16:01:18 -06:00
Satish Balay
6fcfc3bd5a flake8: fix warnings (#5759) 2017-10-13 15:16:58 -06:00
Ondřej Čertík
6c3184820a Use cflags instead of the args variable (#5756)
That way the user can still append things to CFLAGS.
2017-10-13 15:15:06 -06:00
Christoph Junghans
3c7dd367f8 py-espresso: initial commit (#5724) 2017-10-13 12:29:30 -07:00
Christoph Junghans
23e801923d espressopp -> py-espressopp (#5732)
* espressopp -> py-espressopp

* Update package.py
2017-10-13 12:28:36 -07:00
Ondřej Čertík
e76cfbbfd8 Fix m4 to compile with Intel (#5728)
Fixes #5705.
2017-10-13 11:20:49 -06:00
Yifan Zhu
8ffe18f1dc r-biostrings: added versioned dependency on r (#5667) 2017-10-13 07:51:30 -06:00
Yifan Zhu
ce1e5e3098 r-zlibbioc: added versioned dependency on r (#5674) 2017-10-13 07:50:10 -06:00
Denis Davydov
b8c1ce43fa trilinos / oce : add missing if before calling macOS_version (#5743)
* trilinos: add missing if before calling macOS_version

* oce: add missing if before calling macOS_version
2017-10-13 07:49:18 -06:00
Yifan Zhu
9716a6f37f r-readr: created new package (#5741) 2017-10-13 07:47:43 -06:00
Yifan Zhu
350624a231 r-dorng: created new package (#5740) 2017-10-13 07:47:01 -06:00
Yifan Zhu
9f3e055e8b r-stringr: added list_url and version 1.2.0 (#5738) 2017-10-13 07:46:29 -06:00
Yifan Zhu
525b69bbad r-stringi: added list_url and version 1.1.5 and 1.1.3 (#5737) 2017-10-13 07:45:26 -06:00
Yifan Zhu
0b117a03c6 r-summarizedexperiment: created new package (#5734) 2017-10-13 07:45:05 -06:00
Yifan Zhu
501ebe6706 r-yaqcaffy: added list_url and versioned dependency on r (#5730) 2017-10-13 07:44:26 -06:00
Denis Davydov
65f12c8160 slepc: refine version constraints for petsc 3.8 (#5752) 2017-10-13 07:11:17 -06:00
Denis Davydov
22ef8efce9 openblas: remove extra develop version (#5750) 2017-10-13 12:10:05 +02:00
Denis Davydov
b182e2334d gettext: fix prefix (#5749) 2017-10-13 10:52:55 +02:00
Brian Van Essen
bd185b8146 Lbann flags (#5747)
* Fixed the datatype flag in the LBANN package.  Also added develop
version to OpenBLAS.

* Fixed where the datatype flag should be set.
2017-10-12 20:23:38 -06:00
Yifan Zhu
f2a6685d8c r-gcrma: added versioned dependency on r (#5670) 2017-10-12 16:18:30 -06:00
Yifan Zhu
d4906169e0 r-simpleaffy: added versioned dependency on r (#5673) 2017-10-12 16:18:15 -06:00
Satish Balay
59163f9750 petsc: add in maintainers (#5729) 2017-10-12 15:09:47 -06:00
David Hows
8ff8b7476c Add the option for a versioned layout to boost (#5709) 2017-10-12 12:51:39 -06:00
Audrey Thoma
36ed96e7dd kaks-calculator: new package (#5725)
* kaks-calculator: new package

* kaks-calculator: new package

* fixing homepage
2017-10-12 12:47:11 -06:00
Satish Balay
98c2184bd3 petsc: update to latest 3.8 version [and include 3.7.7] (#5723)
Also fix flake8 warning "import os should be before import sys"
2017-10-12 12:46:00 -06:00
Jon Rood
c0b2e7db73 Add OpenFAST package (wind turbine simulation tool). (#5662)
* Add OpenFAST package (wind turbine simulator).
* Adding maintainer to openfast package.
* Fixing copyright date.
2017-10-12 11:42:51 -07:00
Denis Davydov
1b53e82348 various fixes for macOS high sierra (#5647)
* various fixes for macOS high sierra

* add macOS_version() helper function

* flake8 fixes

* update oce and trilinos

* fix bison
2017-10-12 11:41:57 -07:00
Carlos Bederián
db149876a4 samtools: add version 1.6 + some fixes (#5715)
* htslib: add version 1.6

* samtools: add version 1.6, remove zlib dependency

* bcftools: add version 1.6, switch to using standalone htslib
2017-10-12 10:08:31 -06:00
Audrey Thoma
87c65fafa9 minimap2: new package (#5722) 2017-10-12 10:07:42 -06:00
David Hows
90cd075277 Initial version of libpcap (#5710)
Add a package script for libpcap with the current version (1.8.1)
2017-10-12 07:00:21 -06:00
Yifan Zhu
e807397074 r-affy: added versioned dependency on r (#5660) 2017-10-11 19:49:48 -06:00
Yifan Zhu
36eba3bf58 r-affyio: added versioned dependency on r (#5661) 2017-10-11 19:49:28 -06:00
Yifan Zhu
db0fec4d09 r-biocinstaller: added versioned dependency on r (#5663) 2017-10-11 19:49:08 -06:00
Yifan Zhu
4e8ac1d525 r-matrixstats: created new package (#5682) 2017-10-11 19:48:39 -06:00
Yifan Zhu
5e41ad6fed r-biocgenerics: added version 0.22.1 and added versioned dependency on r (#5683) 2017-10-11 19:48:19 -06:00
Yifan Zhu
8d48f07de1 r-genomeinfodbdata: added versioned dependency on r (#5685) 2017-10-11 19:48:00 -06:00
Yifan Zhu
a04e95a492 r-genomeinfodb: created new package (#5695) 2017-10-11 19:47:03 -06:00
Yifan Zhu
dc95dddd61 r-genomicranges: added new package (#5697) 2017-10-11 19:45:03 -06:00
Yifan Zhu
c93ecda872 r-futile-options: created new package (#5699) 2017-10-11 19:43:53 -06:00
Yifan Zhu
4af446d7f4 r-lambda-r: created new package (#5700) 2017-10-11 19:43:33 -06:00
Yifan Zhu
f8db73d567 r-futile-logger: created new package (#5701) 2017-10-11 19:43:15 -06:00
Yifan Zhu
01e104dfcb r-rsamtools: created new package (#5702) 2017-10-11 19:42:55 -06:00
Yifan Zhu
670463e95a r-biocparallel: created new package (#5703) 2017-10-11 19:42:25 -06:00
Yifan Zhu
e08e7af34e r-delayedarray: created new package (#5704) 2017-10-11 19:42:04 -06:00
Yifan Zhu
9a2ef4c4b3 r-biomart: added versioned dependency on r (#5666) 2017-10-11 19:41:08 -06:00
George Hartzell
124bdfb910 Strelka depends on boost 1.56.0 *or newer* (#5690)
Relax/correct the constraint on the version of boost used
by Strelka to match the docs.
2017-10-11 17:21:26 -06:00
Denis Davydov
35a62f715b dealii: minor fixes (#5687)
* dealii: fix minor bug in Assimp config

* dealii: request sundials without pthreads
2017-10-11 15:09:39 -06:00
Christoph Junghans
cfc13dec9f Add a bundle package for the ECP proxy applications suite (#5689)
* Add a bundle package for the ECP proxy applications suite

* Update package.py
2017-10-11 13:39:30 -06:00
健美猫
9e95e8394e Add a package: dmlc/mxnet. (#3579)
* Add dmlc/mxnet packags.

* Build mxnet+cuda+opencv with GCC-4.8.5 and GCC-5.4.0.

* Build mxnet version 0.10.0, 0.10.0.post1 and 0.10.0.post2.

* Add component version constrain for mxnet 0.10.0.x .

* Go through flake8.

* Replace commit hash with commit date as package version.

* Go throught Travis-CI.

* Update submodule version for 0.10.0.post2.

* Add openmp variant for dmlc-core and mxnet.

* Refine variant handling.

* Fix filter_file for dmlc-core.

* Cut long strings into multiple lies due to PEP8 requirements.

* Fix for PEP8.

* Add CUB_INCLUDE.

* Add py-mxnet: Python binding for MXNet.

* Remove distutils.dir_util.

* Add the profiler variant for mxnet.

* Add a shared variant for nnvm.

* Set USE_OPENMP to OFF by default.

* Fix flake8 errors.

* Fix flake8 issues.

* flake8 issues again.
2017-10-10 13:56:26 -07:00
Christoph Junghans
ef822453b9 Adding flang - a llvm based Fortran compiler (#5459)
* flang: initial commit

* flang: added symlink to clang's flang

* add flang wrapper

* flang wrapper: inject rpath as well

* flang wrapper: PATH -> -B
2017-10-10 13:52:31 -07:00
Christoph Junghans
88b515ede8 ninja: add v1.8.2 (#5625) 2017-10-10 12:50:56 -07:00
Massimiliano Culpo
a3bbe066b3 plumed: reworked patching applications, added new version (#5680)
closes #5506

The application of patches to upstream executables has been reworked
according to the suggestions of the main developer in #5506. In
particular we are not maintaining a dictionary that maps plumed
versions to the versions of patchable executables, and we are using a
non-interactive command to patch applications.

All the comments on substituting plumed at run-time do not apply here,
since we use RPATH and we want to maintain a 1:1 relationship between
the DAG hash and the plumed library used.
2017-10-10 12:35:53 -07:00
Audrey Thoma
e3053d7425 snap-korf: new package (#5589) 2017-10-10 11:09:31 -07:00
Jon Rood
f2b49d8f66 Adding openfast variant to nalu. (#5675) 2017-10-09 20:10:47 -06:00
lingnanyuan
35583f48f4 r-adsplit: Create new package and update version for its dependencies. (#5640)
* r-adsplit: Create new package.

* r-rlang: Update version.

* r-s4vectors: Update version.
2017-10-09 17:10:29 -06:00
Audrey Thoma
a8cd92a2e4 switching downloads to git (#5659) 2017-10-09 17:07:13 -06:00
lingnanyuan
196b82f2c7 r-affycompatible: Create new package. (#5664) 2017-10-09 17:05:53 -06:00
lingnanyuan
ef1f71447e r-affydata: Create new package. (#5665) 2017-10-09 17:05:21 -06:00
lingnanyuan
1f05e9ae58 r-affycontam: Create new package. (#5668) 2017-10-09 17:04:51 -06:00
George Hartzell
ab2c7573c1 strelka: new package (#5632)
* Add package for strelka@2.8.2

* Fix flake8 complaints
2017-10-09 17:02:44 -06:00
George Hartzell
0d1c36e559 Add package for aspell and ass't dictionaries (#3890)
* Add package for aspell and ass't dictionaries

Add a package definition for aspell.

Add a handful of dictionaries to convince myself that the support for
a bunch of dictionaries works.

* Flake8 cleanup

* Use six's version of urlparse

`urlparse` is not python3 friendly.  This works around it (stolen from
`.../cmd/md5.py`).

* Fix incorrect trimming regexp

* Clean up dictionary build

- more parsimonious use of `which` (`make()` has already been made)
- use `sh` instead of `bash`

* Use a helper method to generate info for variants

I figured out my issues with static methods.  I *think* that it this
is pythonic.

* Convert aspell to an extendable package

Convert aspell to be extendable and rework the dictionaries to be
extensions.

As it stands, there's a great deal of cut and paste in the
dictionaries, I'll abstract that out next.

The {de,}activate methods copy a great deal of code out of
package.py.  Perhaps there's a better way....

* Create AspellDictPackage and use it for the dictionaries

Reduce the repeated code, pull it into a base class.

I'm confused about why 'from spack import *' wasn't more useful in the
base class.

* Oops, -de & -es should be AspellDictPackages too

* Typo: pakcage -> package

* Address some commentary

* Update copyright dates, 2016->2017
2017-10-09 14:14:19 -07:00
Aaron Fisher
5ccc9c17dc Added mfem v3.3.1-rc1 to the mfem package. (#5644) 2017-10-09 21:48:25 +02:00
Axel Huebl
4ba7359d55 libpng: zlib flags more elegant (#5656) 2017-10-09 21:46:10 +02:00
Christoph Junghans
57643ae84e espressopp: added v1.9.5 (#5652) 2017-10-08 18:16:56 -07:00
Piotr Luszczek
1b5410b87b Add PLASMA package (#5540) 2017-10-08 17:59:41 -06:00
Pramod S Kumbhar
32d183af05 Fix node-js : requires openssl min 1.0.2 (#5650) 2017-10-08 17:04:09 -06:00
Denis Davydov
5ed457759c hypre: add 2.12.1 (#5653) 2017-10-08 07:27:25 -06:00
George Hartzell
ee6d21e311 adding http2 support (#5628)
Requires nghttp2 libraries
2017-10-07 09:58:56 -06:00
lingnanyuan
73bb34ad6e r-affycomp: Create new package. (#5642) 2017-10-06 20:13:57 -06:00
lingnanyuan
a755c47fb1 r-affxparser: Create new package. (#5641) 2017-10-06 20:13:38 -06:00
Yifan Zhu
cf94e4140b r-genomeinfodbdata: created new package (#5639) 2017-10-06 20:13:09 -06:00
Yifan Zhu
62538e3d37 r-hms: created new package (#5638) 2017-10-06 20:12:59 -06:00
William Scullin
3d8d3e8882 qmcpack: new package (#4907)
This adds QMCPACK along with patches to Quantum Espresso for using Quantum Espresso in QMCPACK workflows.
2017-10-06 13:51:18 -07:00
George Hartzell
d05f98d405 Nghttp2 new package (#5627)
* nghttp2 library package

Added for dependencies

* Update package.py

* Removed useless code

* Flake8 fix
2017-10-06 13:59:56 -06:00
George Hartzell
a659f0f8f4 Add a package for VarDictJava@1.5.1 (#5626)
This is a simple package that drops their shell wrapper into
prefix.bin and their jar files into prefix.lib.

The approach comes from the picard package.
2017-10-06 13:58:34 -06:00
George Hartzell
202c66d90c The silver searcher: new version (#5630)
* Updating ag to the latest version

* Pretty by request

* Restore url to previous value

There *is* an https version available, but I've also been told
to not just update the url when adding new version.  I'm following
the latter advice and trusting security to the digest.
2017-10-06 13:56:58 -06:00
Massimiliano Culpo
2b2a5ca7bf git + luafilesystem: minor fixes (#5635)
* git: setup_dependent_environment won't fail for external packages

* luafilesystem: relax the request on git (it seemed overly restrictive)
2017-10-06 13:56:14 -06:00
George Hartzell
68011bde39 maven: new version (#5631)
* Adding maven v3.5.0

Updating package file to include later version of maven but still signifying a preference for the older

* removing specific preference flag
2017-10-06 13:53:56 -06:00
Michael Kuhn
4065ef2106 ncl: Fix temp directory and depend on esmf (#5636)
* ncl: Fix temp directory

Currently, ncl is configured using a transient temp directory. This
leads to warnings such as this when executing ncl later on:

warning:"/tmp/ncl_ncar_xxxxxx" tmp dir does not exist or is not writable:
NCL functionality may be limited -- check TMPDIR environment variable

As this also breaks some functionality, use the system temp directory
instead (typically /tmp).

* ncl: Depend on esmf

esmf is required for some ncl scripts (such as ESMF_regridding.ncl).
2017-10-06 13:53:05 -06:00
George Hartzell
b9d7903cdb Add link dependency on xproto to xau (recent dependency mechanics changes?) (#5624)
* Add link dependency on xproto to xau

The libxcb build was failing like so:

```
1 error found in build log:
     [ ... ]
     131   checking whether to build developer documentation... yes
     132   checking for doxygen... /usr/bin/doxygen
     133   checking for dot... /usr/bin/dot
     134   checking for CHECK... no
     135   checking for XCBPROTO... yes
     136   checking for NEEDED... no
  >> 137   configure: error: Package requirements (pthread-stubs xau >= 0.99.2) were not met:
     138
     139   Package 'xproto', required by 'xau', not found
     140
     141   Consider adjusting the PKG_CONFIG_PATH environment variable if you
     142   installed software in a non-standard prefix.
     143
```

This adds a link dependency on libxproto that allows the libxcb build to
succeed.

* Change more build deps to build, link

These were also necessary for emacs+X to build.

* Fix flake8 complaint
2017-10-05 16:53:12 -06:00
Audrey Thoma
17139b575d fsl: new package (#5605) 2017-10-05 11:57:57 -07:00
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