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4832 commits

Author SHA1 Message Date
Ben Boeckel
13b669de8e view: test that extension paths exist 2017-11-02 18:45:40 -07:00
Ben Boeckel
41dfba0ba1 extension1: add a second version 2017-11-02 18:45:40 -07:00
Ben Boeckel
a7925bb927 bdftopcf: require xproto and fontsproto at build time (#6112) 
These are technically "link" depends of libxfont, but they have no
actual libraries.

Fixes #5936.
 2017-11-02 15:47:18 -06:00
lingnanyuan
13f1781bea Add package r-reportingtools and update url for its dependencies. (#6071) 
* r-reportingtools: Create new package.

* r-go-db: Update url.

* r-gseabase: Update url.

* r-pfam-db: Update url.
 2017-11-02 14:21:32 -06:00
Michael Kuhn
d1db161aeb adios: Fix hdf5 and sz dependencies (#6016) 
- hdf5's +hl variant is required because the build uses libhdf5_hl.
- sz is only compatible up to version 1.4.10 because the library has
  been renamed to libSZ in 1.4.11.
 2017-11-02 13:41:25 -06:00
Brice Goglin
3a1b013291 hwloc: add version 1.11.8 (#6099) 
Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
 2017-11-02 13:40:46 -06:00
Audrey Thoma
f9341857c7 arlecore: new package (#6109) 2017-11-02 13:40:03 -06:00
Christoph Junghans
c4db3d384e gromacs: add develop version (#6098) 2017-11-02 15:16:21 +01:00
Adam J. Stewart
e47ceefc43 sundials+hypre depends on hypre (#6075) 2017-11-02 08:16:43 +01:00
Denis Davydov
11ba60413b the-silver-searcher: add missing dependency (#6095) 2017-11-02 08:10:40 +01:00
Michael Kuhn
61ed583266 xqilla: Use append instead of extend (#6094) 2017-11-02 08:09:24 +01:00
Brian Van Essen
932068d725 Update candle (#6097) 2017-11-01 23:58:55 -06:00
Yifan Zhu
7d0c6361ee r-getoptlong: created new package (#6069) 2017-11-01 19:09:54 -06:00
Yifan Zhu
f15969d624 r-gtrellis: created new package (#6088) 2017-11-01 19:09:20 -06:00
Brian Van Essen
86b7b84ddf LBANN flags and OpenCV variant (#5951) 
* Fixed the datatype flag in the LBANN package.
Fixed where the datatype flag should be set.

* Added variant to OpenCV to disable building DNN support

* Fixed a bug in how the elemental package tries to find its Fortran
library.  The current method does not work with Intel compilers.

* Added necessary paths for cuDNN and CUB.

* Addressed flake8 issues in Elemental package.

* Fixed several flake8 errors.  Added variant to build with or without
support for arbitrary-precision floating point arithmetic.

* Added the proper CMake flag when MPFR support is disabled.

* Fixed a bug in how the cudnn path was being set when there was no
cudnn requested.  Also requested that OpenCV is built without eigen
support.

* Fixed another bug where a dependency may not be there and thus should
not be always checked.
 2017-11-01 17:25:28 -07:00
Michael Kuhn
0d624eac55 lua: Build a shared library (#6008) 
Patch is inspired by Arch Linux and Homebrew.
 2017-11-01 17:10:14 -06:00
Yifan Zhu
f3af8272f5 r-circlize: new package (#6087) 2017-11-01 17:08:46 -06:00
lingnanyuan
ef240f59b8 r-alsace: Create new package. (#6064) 2017-11-01 17:04:56 -06:00
Yifan Zhu
26ade0c9ae r-globaloptions: new package (#6068) 2017-11-01 17:04:38 -06:00
lingnanyuan
a05cca49d8 r-affycoretools: Create new package and its dependency r-ff. (#6082) 
* r-ff: Create new package

* r-affycoretools: Create new package.

* r-ff: update url.
 2017-11-01 17:04:17 -06:00
lingnanyuan
541818ed06 r-agimicrorna: Create new package. (#6083) 2017-11-01 17:03:48 -06:00
Yifan Zhu
616a43b76d r-complexheatmap: created new package (#6084) 2017-11-01 17:03:30 -06:00
Yifan Zhu
ebff5086d7 r-shape: created new package (#6086) 2017-11-01 17:03:15 -06:00
Yifan Zhu
7fb6fbea54 r-pmcmr: new package (#6085) 2017-11-01 17:02:58 -06:00
Brian Van Essen
0c075b4923 Opencv eigen (#6014) 
* Added a package for the MDAnalysis toolkit.

* Changed dependency for the eigen library to not include support for
multiple-precision (arbitrary-precision) floating point arithmetic,
since OpenCV does not support these data types.

* Fixed incorrect implementation
 2017-11-01 13:50:06 -07:00
Mark Grondona
165e6bfe5f flux: update flux-core to v0.8.0 (#5914) 
* dockbook: remove update to dependent environment

Remove override of setup_dependent_environment in both docbook-xml
and docbook-xsl, which seems to generate a warning from spack about
"Suspicious requests to set or unset 'XML_CATLOG_FILES' found."

* flux: update version/dependencies to 0.8.0

Update flux-core to v0.8.0. Clean up dependencies and remove unneeded
extra invocation of ./autogen.sh when building from @master.

* flux: modify environment for Lua tests

Modify Spack environment to add `./?.lua` to LUA_PATH so that
fluxometer.lua can be found by tests during `make check` run
from `spack install --tests all flux`

* flux: fix broken flux version when on master

When building @master with spack, the flux version test from
`make check` fails because spack is using a shallow clone. Add
a setup section for @master that calls git pull --depth=50 --tags
to pull down tags and (hopefully) enough information for git-describe
to work properly.
 2017-11-01 08:53:37 -07:00
Satish Balay
445ffc46a1 mfem does not use cmake for builds [anymore] - so remove code corresponding to this dependency. (#6073) 
This enables mfem build on OSX [with xcode/clang compilers]
 2017-11-01 08:52:03 -07:00
Elsa Gonsiorowski
b53adc90f7 MACSio and JSON-CWX packages (#6018) 2017-10-31 19:07:00 -06:00
Patrick Gartung
8a812294e0 Preinstall some llvm shared libraries so tblgen will work. (#5988) 2017-10-31 18:34:33 -06:00
Yifan Zhu
0ecef7d7f8 r-somaticsignatures: created new package (#6065) 2017-10-31 18:31:06 -06:00
lingnanyuan
1ec8f6ea3f r-nloptr: Create new package. (#6063) 2017-10-31 18:30:49 -06:00
lingnanyuan
cfb685aa32 r-ptw: Create new package. (#6062) 2017-10-31 18:29:45 -06:00
lingnanyuan
aa1808c9a1 r-iso: Create new package. (#6061) 2017-10-31 16:17:53 -06:00
lingnanyuan
6af19477ef r-nnls: Create new package. (#6060) 2017-10-31 16:17:36 -06:00
lingnanyuan
77b29288e6 r-als: Create new package. (#6059) 2017-10-31 16:17:21 -06:00
Yifan Zhu
10fcd9382a r-ggbio: new package (#6058) 2017-10-31 16:17:07 -06:00
Bill Williams
f5e68879db Fix spack build for RAJA: master requires submodules (#6052) 
* Fix spack build for RAJA: master requires submodules

* Rename version: git to develop
 2017-10-31 15:08:32 -06:00
Scott Wittenburg
3cb2d5341d Fix incorrect checksum value for adios2 tarball (#6054) 2017-10-31 15:08:08 -06:00
lingnanyuan
6427406fc6 r-gviz: Create new package. (#6043) 2017-10-31 15:06:30 -06:00
Brian Homerding
8a86016bef Added fftw dependency (#6057) 2017-10-31 14:33:01 -06:00
Brian Homerding
180dcfc652 sw4lite: Added -lgfortran and set to serial build (#6055) 
* Added -lgfortran and set to serial build

* Update package.py
 2017-10-31 14:29:06 -06:00
Christoph Junghans
d98e337706
ecp-proxy-suite: add nekbone and candle-benchmarks (#6053) 2017-10-31 13:11:08 -06:00
Christoph Junghans
182c11dd92
nekbone: add v17 (#5978) 2017-10-31 10:47:24 -06:00
Christoph Junghans
178107699c
candle-benchmarks: initial commit (#6020) 2017-10-31 09:11:04 -06:00
Christoph Junghans
ea35f49cdd flang: fixed a typo (#6048) 2017-10-31 14:21:29 +01:00
Nils Deppe
4997291bf4 Add v3.2 of Blaze library (#5992) 2017-10-31 08:33:55 +01:00
George Hartzell
e69542c019 Fix tarball URL's for htslib (#5993) 
A recent update (#5907) to htslib added a different URL for an old
version of htslib.

Now the package is using that URL as the pattern for the newer
versions too.

I have a vague memory of running into this before, that it's a known
issue.

This fixes it by adding an explicit `url_for_version` routine.
 2017-10-30 22:49:52 -06:00
David Gardner
10b27ec788 sundials: update to v3.0.0 (#6004) 2017-10-30 22:49:13 -06:00
Jon Rood
50d932d9f1 Merging netcdf dependency lines in trilinos into one line for better coverage. (#5990) 2017-10-30 22:48:21 -06:00
Satish Balay
f5863d6708 superlu_dist: update to v5.2.2 (#6024) 2017-10-30 22:46:41 -06:00
Yifan Zhu
a31a1fef28 r-progress: new package (#6034) 
* r-progress: created new package

* added version
 2017-10-30 22:43:57 -06:00
Yifan Zhu
a97068a861 r-prettyunits: created new package (#6033) 2017-10-30 22:43:20 -06:00
lingnanyuan
6ddba08434 r-seqinr: Update version to 3.4-5 (#6032) 2017-10-30 22:42:51 -06:00
Yifan Zhu
8cc3bcb649 r-ggplot2: dependecy r-scales version should be 0.4.1: (#6031) 2017-10-30 22:42:31 -06:00
Yifan Zhu
fb072d1472 r-scales: added dependencies and version 0.5.0. (#6030) 
* r-scales: Update url.

* r-scales: added version 0.5.0 and dependencies
 2017-10-30 22:42:05 -06:00
lingnanyuan
7e4ac9a559 r-segmented: Update version to 0.5-2.2 (#6029) 2017-10-30 22:41:32 -06:00
Yifan Zhu
34c6ff10e9 r-ggally: new package (#6036) 
* r-ggally: created new package

* r-ggally: version modified
 2017-10-30 22:41:12 -06:00
lingnanyuan
65785cc3f5 r-speedglm: Create new package. (#6035) 2017-10-30 22:40:48 -06:00
lingnanyuan
a4138b6041 r-alpine: Create new package. (#6037) 2017-10-30 22:40:25 -06:00
Yifan Zhu
22f9125164 r-ensembldb: created new package (#6038) 2017-10-30 22:39:54 -06:00
Yifan Zhu
2a7027e2cc r-pcamethods: created new package (#6041) 2017-10-30 22:39:29 -06:00
Yifan Zhu
cbb433655c r-proxy: created new package (#6039) 2017-10-30 22:39:05 -06:00
lingnanyuan
8271434632 r-backports: Create new package. (#6040) 2017-10-30 22:38:35 -06:00
lingnanyuan
81d3c9fdc6 r-biovizbase: Create new package. (#6042) 2017-10-30 22:38:10 -06:00
Abhinav Bhatele
b37c8fef74 ecp-proxy-apps: release number changed to 1.0 (#6049) 2017-10-30 22:37:09 -06:00
Abhinav Bhatele
347c76b7a0 comd: update the git repo (#6027) 
git repo has moved from exmatex to ECP-copa
 2017-10-30 14:47:16 -06:00
George Hartzell
e6bc45a04a Add bowtie2@2.3.0, fix dependencies and sbangs (#5834) 
* Add bowtie2@2.3.0, fix dependencies and sbangs

Add support for bowtie2@2.3.0

- digest
- a patch for 2.3.0 that parallels the existing package.  Truth be
  told it builds (for me) without this, but I'm assuming that they're
  there for a reason...).
- tune up dependencies
  - need tbb
  - don't need readline or zlib

Several things were installed with sbang's that use `/usr/bin/env` to
fine perl or python.  Fix the dependency and clean up the sbang lines.

* Fix python exe name, avoid path banging

I'd cut and pasted the python bit from the perl bit and missed one
reference to perl.

While I'm there, use the cleaner `spec['perl'].command` instead of
banging together the path from its bits.

* Fix up the "when" constraints on the dependencies

Get the edge cases right.

- 2.2.5 doesn't need tbb, 2.3.[01] do.
- 2.3.1 needs readline and zlib.
 2017-10-29 15:40:00 -06:00
Denis Davydov
957ded209a add updated 2017 versions of Intel packages (#5957) 2017-10-29 15:38:10 -06:00
mmwolf
73fb02229a Changed from setting C compiler to setting C++ compiler (#6011) 2017-10-29 07:42:27 -06:00
Denis Davydov
f6a8ae230e dealii: remove bzip2 dependency for newer versions (#6022) 2017-10-29 07:39:51 -06:00
Yifan Zhu
56c7832789 r-iranges: changed url to git and added versioned dependency on r (#5971) 2017-10-28 12:14:33 -06:00
Audrey Thoma
f340333e6e r-geomorph and other r fixes (#5961) 2017-10-28 12:13:38 -06:00
lingnanyuan
57611397c9 r-e1071: Add list_url. (#5986) 2017-10-28 12:12:52 -06:00
Michael Kuhn
b43e2d2546 likwid: Update checksum (#6007) 2017-10-28 12:12:21 -06:00
Yifan Zhu
43c1bb5f30 r-organismdbi: new package (#5997) 2017-10-28 12:11:44 -06:00
lingnanyuan
3eab6ed4b2 r-aldex2: Create new package. (#6015) 2017-10-28 12:10:22 -06:00
Christoph Junghans
167f7d0cdd
legion: add v17.10.0 (#6019) 2017-10-28 12:09:39 -06:00
Audrey Thoma
edae3ceae7 fixing abyss (#5973) 2017-10-28 17:05:52 +02:00
Sergey Kosukhin
5ebddcd5e3 Bugfix: from_list_url(). (#5780) 
This fixes a bug in from_list_url where it was referring to a method
which no longer exists. This also adds a test for the from_list_url
function.
 2017-10-27 17:41:41 -07:00
Christoph Junghans
95c8ecb6f5
libaec: add v1.0.2 and generic url (#6017) 2017-10-27 18:22:27 -06:00
Matthias Diener
45bfcfa30a Byobu: new package (#5974) 2017-10-27 10:43:45 -07:00
Christoph Junghans
f9599c1772 ecp-proxy-apps: add more package (#6003) 2017-10-27 08:34:52 -06:00
Christoph Junghans
c97bf0486c SWFFT: initial commit (#5953) 
* SWFFT: initial commit

* swfft: fix build target

* swfft: add v1.0

* Update package.py
 2017-10-27 07:20:29 -06:00
Christoph Junghans
13b41cd53c comd: add v1.1 (#5994) 
* comd: add v1.1

* Update package.py

* remove serial variant, now ~mpi

* Update package.py
 2017-10-27 07:20:18 -06:00
lingnanyuan
222fee1cb3 r-graph: Create new package. (#5958) 2017-10-27 08:34:33 +02:00
lingnanyuan
f244653496 r-category: Create new package. (#5959) 2017-10-27 08:34:16 +02:00
lingnanyuan
715a679245 r-methodss3: Create new package. (#5960) 2017-10-27 08:32:20 +02:00
lingnanyuan
737f9eee5c r-oo: Create new package. (#5962) 2017-10-27 08:31:46 +02:00
lingnanyuan
f676d8f3d7 r-utils: Create new package. (#5964) 2017-10-27 08:31:26 +02:00
lingnanyuan
3bb4572e81 r-pfam-db: Create new package. (#5965) 2017-10-27 08:27:19 +02:00
lingnanyuan
95ece343c4 r-oligoclasses: Create new package. (#5966) 2017-10-27 08:26:25 +02:00
Yifan Zhu
3ea6a11043 r-interactivedisplaybase: created new package (#5967) 2017-10-27 08:26:02 +02:00
lingnanyuan
c672b2b191 r-annotationforge: Create new package. (#5968) 2017-10-27 08:25:12 +02:00
lingnanyuan
57528fddbb r-gostats: Create new package. (#5969) 2017-10-27 08:24:49 +02:00
Audrey Thoma
835e6107fe r-mcmcglmm: new package (#5970) 2017-10-27 08:24:28 +02:00
Yifan Zhu
7b0fd6510c r-annotationhub: created new package (#5972) 2017-10-27 08:23:25 +02:00
Denis Davydov
c2094a11e3 gnuplot: add 5.2.0 and 5.0.7 (#5979) 2017-10-27 08:20:34 +02:00
lingnanyuan
dc8a0e8410 r-deseq2: Create new package. (#5981) 2017-10-27 08:16:40 +02:00
lingnanyuan
1de2109a5a r-agdex: Create new package. (#5983) 2017-10-27 08:16:04 +02:00
lingnanyuan
82b1731ded r-agilp: Create new package. (#5984) 2017-10-27 08:15:39 +02:00