Commit graph

5783 commits

Author SHA1 Message Date
George Hartzell
ec3eabfc7a Add package for BATS (#3611)
Add package for the BASH Automated Testing System.
2017-03-28 21:36:12 -05:00
George Hartzell
9385659aa1 bowtie2: add support for version 2.3.1 (#3599)
* Add support for 2.3.1

Updated digest and added a dependency on tbb.

* Cleanup patch name and add description
2017-03-28 21:35:46 -05:00
George Hartzell
d6cbae81c7 Update/samtools (#3595)
* Update samtools family to 1.4

* simple cleanup

* Make bzip depends_on for future versions too
2017-03-28 21:34:41 -05:00
George Hartzell
70ec06949c New package: ncftp client (#3603)
* Add package for ncftp

* Flake8 cleanups
2017-03-28 21:33:59 -05:00
George Hartzell
d94757238a New package: staden-io-lib (#3604)
* Add package for staden-io-lib

* Flake8 cleanups
2017-03-28 21:33:34 -05:00
George Hartzell
bdf0baead7 New package: mummer (#3606)
* Add package for mummer

Blocked on https://github.com/LLNL/spack/pull/3555.

* Make "check" step optional and flake8 cleanups
2017-03-28 21:27:20 -05:00
George Hartzell
81a0881a57 new package: pigz (#3612)
* Add package for pigz

* Whitespace

* Remove leftover instructions (oops...)

* Flake8 cleanup

* Convert to MakefilePackage
2017-03-28 21:15:30 -05:00
George Hartzell
e5eb8e34c5 new package: blat (#3610)
* Add package for blat

* Whitespace cleanup

* Flake8 cleanup
2017-03-28 21:14:26 -05:00
George Hartzell
1e5da65d65 Add packages for miniconda[23] (#3613) 2017-03-28 21:13:46 -05:00
George Hartzell
36f80bdfa4 Add support for version 20170322 (#3598) 2017-03-28 18:56:21 -05:00
George Hartzell
a9025e3283 Add version info for 7.4.1 (#3600) 2017-03-28 18:55:25 -05:00
George Hartzell
212b342fd3 Add support for v8.0.0503 (#3596) 2017-03-28 18:51:30 -05:00
George Hartzell
5f3e9a791f Nextflow versions 0.24.1 and 0.23.3 (#3597)
Add support for nextflow versions 0.24.1 and 0.23.3.
2017-03-28 18:50:21 -05:00
sknigh
42f9040dfe fix for #3588 (#3589)
* fix for #3588

* set 'build_directory' variable instead
2017-03-28 12:59:24 -05:00
健美猫
8378d659e7 Add a package: cub. (#3584) 2017-03-28 12:46:47 -05:00
healther
41cfb811f0 add package double-conversion (#3585) 2017-03-28 12:29:05 -05:00
healther
98d67bd060 Add new version to glog (#3586) 2017-03-28 12:28:30 -05:00
sknigh
f6b6e397cb Add SST/macro and Dumpi trace packages (#3025)
* Added packages for Structural Simulation Toolkit and Dumpi trace

* sst-dumpi deps

Remove extraneous dependency from sst-dumpi

* Removed redundant function and fake-url from sst-dumpi package

* Fixed URL, Added git branches, requested changes

sst-dumpi version listed as 6.1, made an upstream change to 6.1.0
sst-macro and sst-dumpi can be installed as v6.1.0 and master branch

* Added bootstrap. Tweaked URLs and description
2017-03-28 12:28:05 -05:00
Todd Gamblin
dead67ae56 Restore newlines to easy-install.pth files. (#3583)
Previous syntax fix in 8a873bb was not quite right.
2017-03-28 09:32:50 -07:00
Todd Gamblin
782f29bc4b Fix bug in spack find for installations with unknown namespaces. (#3573)
- Spack find would fail with "unknown namespace" for some queries when a
  package from an unknown namespace was installed.

- Solve by being conservative: assume unknown packages are NOT providers
  of virtual dependencies.
2017-03-28 08:43:43 -07:00
Todd Gamblin
e549daa8ce Bugfix: allow deactivating installs that don't have packages anymore. (#3572)
- deactivate -a wouldn't work if the installation's package was no longer
  available.

- Fix installed_extensions_for so that it doesn't need to look at the
  package.py file.
2017-03-28 08:43:15 -07:00
健美猫
d9ddf2070c Add package kaldi. (#3503) 2017-03-28 09:39:23 -05:00
Erik Schnetter
e9737ee452 googletest: Convert to CMakePackage (#3571)
* googletest: New version 1.8.0

* googletest: Simplify
2017-03-28 09:34:45 -05:00
Denis Davydov
a8c58551ae openblas: raise an error when using unsupported Apple clang (#3577) 2017-03-28 08:14:12 -05:00
Mark Olesen
89d08c5be4 CONFIG: update versions for paraview (#3537)
- drop old TCL support from paraview build.

- add +plugins variant to have include directories installed. This is
  enabled by default since the additional diskspace for includes is
  really minimal and since this also allows re-use of the VTK libraries
  from ParaView without necessarily requiring a separate VTK
  installation.

- +opengl2 is now the default. As per all newer VTK and paraview versions.

BUG: broken install for paraview-5.0.1 with includes and without python

- incorrect conditional for ui_pqExportStateWizard.h when python is
  disabled and includes are to be installed.
  gcc compiler detection patch.
  These have both been fixed in paraview 5.3.0

ENH: refactor as a CMakePackage.

- Note that "spack install paraview" works as expected, but
  "spack build paraview" fails in weird unrelated ways.
2017-03-28 08:09:22 -05:00
Peter Doak
c20cd73b4a this builds cvs CentOS Linux release 7.2.1511 (#3574) 2017-03-27 14:33:22 -07:00
Gregory Lee
1cc2d22268 Merge pull request #3570 from LLNL/packages/elfutils-preferred-version
Make 0.163 the preferred version of elfutils.
2017-03-27 11:15:46 -07:00
Gregory Lee
8a873bbd8d Fix easy-install.pth syntax (#3569) 2017-03-27 10:56:55 -07:00
Todd Gamblin
394b78637d Make 0.163 the preferred version of elfutils.
- later versions do not seem to work well with libdwarf.
2017-03-27 10:14:49 -07:00
George Hartzell
625a1634bb Update to version 0.4.8-1 (#3568) 2017-03-27 11:24:51 -05:00
George Hartzell
9f19cb4193 Bugfix/gnutls (#3565)
* Fix nettle dependency

GnuTLS requires a nettle from the 2.7 series, won't work
with 3.x (so sayeth configure when it crashes...).

* Fix configure symlinking GNUmakefile to itself

I'm confused about how this ever worked, but....

As configure runs, it does something like this:

```
config.status: linking /home/hartzelg/tmp/spack/var/spack/stage/gnutls-3.3.9-uq2u4ecucncv2l3akran765aystyvkys/gnutls-3.3.9/GNUmakefile to GNUmakefile
```

and since that is the cwd the build crashes with:

```
==> 'make' '-j28'
make: GNUmakefile: Too many levels of symbolic links
make: stat: GNUmakefile: Too many levels of symbolic links
make: *** No rule to make target `GNUmakefile'.  Stop.
```

Since the comment in the configure script points out that the
GNUmakefile is "only for the maintainer" I've just commented out the
bit that leads to the symlinking.

Builds for me on CentOS 7.  (I do have a recent-ish set of auto-*
things in my patch via linuxbrew)

* Wordsmith

* Fix symbolic link problem properly

Autotools magic.  See #3565 for the details.

* Flake8 cleanup

* Add some headroom on the version number constraint

We really want < 3.0 but there's not a good way to express it.

We'd like to avoid having to update the file if they release 2.7.2.

This seems like a good compromise.
2017-03-27 10:29:56 -05:00
Mark Olesen
f3ee4ec5bd CONFIG: update qt package to build qt-5.7.1 (#3535)
- adjusted formatting to reduce some flake8 complaints
2017-03-27 08:29:33 -05:00
健美猫
a623a146de fftw: Add 3.3.6-pl2, remove 3.3.6-pl1. (#3566) 2017-03-27 07:55:16 -05:00
Mark Olesen
1c73f9d92f ENH: add int64 variant to scotch (as per metis +int64) (#3536)
BUG: provide patch for scotch 6.0.4 if building non-threaded

- corresponds to issue #20179 from the scotch issue trackter
2017-03-27 07:48:14 -05:00
George Hartzell
dd79630464 Update texlive digest/md5 (sigh...) (#3564) 2017-03-26 19:26:33 -05:00
George Hartzell
2d78b3113c Nettle: new version (#3563)
gnutls needs nettle from the 2.7 series.  Might as well give it
the latest.
2017-03-26 19:26:07 -05:00
Denis Davydov
2b3ce576a5 tbb: add 2017.5 (#3560) 2017-03-26 09:38:18 +02:00
Denis Davydov
b8486f413a mumps: add 5.1.1 (#3557) 2017-03-26 09:33:44 +02:00
Denis Davydov
a14f9491db hypre: add 2.11.2 (#3556) 2017-03-26 09:32:49 +02:00
Denis Davydov
57ef184254 superlu-dist: add 5.1.3 (#3559) 2017-03-26 09:31:32 +02:00
Denis Davydov
1e9eae4bfa suite-sparse: add 4.5.4 (#3558) 2017-03-26 09:26:57 +02:00
George Hartzell
bfd2db0c76 Add url_for_version and depends_on('libiconv') (#3555)
* Add url_for_version and depends_on('libiconv')

Fetching is broken.  See https://github.com/LLNL/spack/issues/3554.

libgd, when used in gnuplot at least, needs a dependency
on libiconv.

* Undo change from debugging pokery
2017-03-25 20:06:09 -05:00
Michael Kuron
55300d1181 pnfft: new package (#2646)
* pnfft: new package

* Convert some packages with overridden install from AutotoolsPackage to Package

* pnfft: fix URL

* Switch FFTW-derived packages back to AutotoolsPackage

* Disable unneeded build phases in FFTW and derived packages

* Separate build phases for FFTW and derived packages

* Fix broken merge

* fftw: pfft_patches for 3.3.6

* fftw: address @adamjstewart’s review comments
2017-03-25 14:27:52 -05:00
Brian Van Essen
3af971165a Added a package for Nvida NCCL (#3552) 2017-03-24 17:53:16 -07:00
Denis Davydov
61d01a71dd make git fetching quite (#3180)
also output repo and branch/commit/tag in one line
2017-03-24 17:37:47 -07:00
Adam J. Stewart
6461737bba Add latest version of util-linux (#3551) 2017-03-24 16:44:54 -05:00
Adam J. Stewart
821155470c Add mozjs package (#3550) 2017-03-24 16:31:59 -05:00
Adam J. Stewart
c97d79b150 Add old version of zlib (#3549) 2017-03-24 16:31:31 -05:00
Adam J. Stewart
5297d3d2ff Add NSPR package (#3548) 2017-03-24 16:23:01 -05:00
Adam J. Stewart
78301396f0 Add linux-headers package (#3547) 2017-03-24 16:22:36 -05:00