Commit graph

9162 commits

Author SHA1 Message Date
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
becker33
5d13f236b4 Fix setup for changes to dirty flag (#5592)
* Pass dirty arg through setup to setup_package
2017-10-09 10:01:55 -07:00
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
scheibelp
b08d457dfd Don't check package.installed in _mark_concrete if value=True (#5634)
* spec and spec.package.spec can refer to different objects in the
database. When these two instances of spec differ in terms of
the value of the 'concrete' property, Spec._mark_concrete can
fail when checking Spec.package.installed (which requires
package.spec to be concrete). This skips the check for
spec.package.installed when _mark_concrete is called with
'True' (in other words, when the database is marking all specs
as being concrete).

* add test to confirm this fixes #5293
2017-10-06 14:23:28 -07:00
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
Jimmy Tang
c6e7fb25a4 Fix formatting typo (#5622) 2017-10-05 10:58:51 -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
becker33
04a4ac68d5 Identify the flag handlers feature as beta (#5609)
The flag-handling logic added in #4421 may change semantics, so this
commit adds a warning to the documentation for this feature.
2017-10-04 18:32:13 -07:00
becker33
328ab328be Fix module loads (#5599)
Fixes #5455

All methods within setup_package use an EnvironmentModifications object
to control the environment. Those modifications are applied at the end
of setup_package. Module loads for the build environment need to be
done after the rest of the environment modifications are applied, as
otherwise Spack may unset variables set by those modules (for example
LD_LIBRARY_PATH).
2017-10-04 18:25:55 -07:00
Massimiliano Culpo
3556eaae7e module files: restricted token expansion + case sensitivity (#5474)
closes #2884
closes #4684

In #1848 we decided to use `Spec.format` to expand certain tokens in
the module file naming scheme or in the environment variable name.
Not all the tokens that are allowed in `Spec.format` make sense in
module file generation. This PR restricts the set of tokens that can
be used, and adds tests to check that the intended behavior is respected.

Additionally, the names of environment variables set/modified by module
files were, up to now, always uppercase. There are packages though that
require case sensitive variable names to honor certain behaviors (e.g.
OpenMPI). This PR restricts the uppercase transformation in variable
names to `Spec.format` tokens.
2017-10-04 18:14:06 -07:00
scheibelp
395000c385 spec.patches: fix dictionary reference (#5608)
This fixes a loop that was iterating through the keys of a dictionary
when it was intending to use the values.
2017-10-04 17:14:58 -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
Massimiliano Culpo
5fa1191d17 Hotfix: maintain patch order while fixing hash
fixes #5587

In trying to preserve patch ordering, #5476 made equality inconsistent
for the added 'patches' variant. This commit maintains the original
weak ordering of patch applications while preserving consistency of
comparisons. The ordering DOES NOT enter the hashing mechanism. It's
supposed to be a hotfix, while we think of a cleaner and more-permanent
solution.
2017-10-04 11:39:25 -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
scheibelp
f53be46186 wrap generator with collection to avoid exhausting it with single iteration (#5586) 2017-10-03 16:47:07 -07:00
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