Commit graph

4490 commits

Author SHA1 Message Date
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
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