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Author SHA1 Message Date
Tom Merrick
bd60f5c927 Fix deleting by r-rmpfr 2017-05-23 10:17:48 -05:00
Milton Woods
4553b1400c Magics with eccodes variant (#4320) 
* magics: use filter_file to avoid using system python in all versions

* magics: add eccodes variant to switch between eccodes and grib-api
 2017-05-23 10:06:59 -05:00
Tom Merrick
1469cfd0e7 Packages/r ergm (#4314) 
* Add mpi support to R

* Add multiple precision math routines to R

* Add packages for r-ergm and it's dependents

* Fixed depends-on types

* Correct flake8 errors
 2017-05-23 10:05:05 -05:00
Massimiliano Culpo
e89c699c06 plumed: fixed compilation on rhel6 (#4318) 
* plumed: fixed compilation on rhel6 with mvapich2 and gcc@5.4.0 (#77)

* plumed: prevent parallel compilation, as it breaks for the newest version
 2017-05-23 10:04:23 -05:00
Tom Merrick
3f6b61d3a5 Merge branch 'packages/r-ergm' into develop 2017-05-23 08:11:53 -05:00
Tom Merrick
1a07fba980 Merge branch 'packages/r-rmpfr' into develop 2017-05-23 08:06:56 -05:00
Tom Merrick
eaa8a4eade Correct Build type 2017-05-23 07:55:10 -05:00
Tom Merrick
4467b90e53 Merge remote branch 'origin/develop' into develop 2017-05-22 16:25:04 -05:00
Tom Merrick
ba6a02cade Correct flake8 errors 2017-05-22 15:24:25 -05:00
Robert D. French
dd73c98d0e Add Microsoft's C++ Rest SDK (#4315) 2017-05-22 15:15:17 -05:00
Tom Merrick
de07180dcd Fixed depends-on types 2017-05-22 13:20:34 -05:00
Tom Merrick
e291d962aa Add packages for r-ergm and it's dependents 2017-05-22 12:34:25 -05:00
Tom Merrick
38ff43dfdc Merge remote branch 'origin/develop' into develop 
Conflicts:
	var/spack/repos/builtin/packages/r-gmp/package.py
	var/spack/repos/builtin/packages/r-rmpfr/package.py
 2017-05-22 08:42:44 -05:00
Milton Woods
8ab8459397 magics: use spack perl instead of system perl (#4310) 2017-05-22 06:45:24 -05:00
Milton Woods
132b3c56bc qt: patch JavaScriptCore to favour internal pcre headers (#4270) 2017-05-21 18:01:26 -05:00
Michael Kuhn
f9203d4281 libdrm depends on pkg-config (#4308) 2017-05-21 13:34:16 -05:00
Milton Woods
ca2755d532 flex: create variant +lex that creates symlinks for lex and libl.{a,so} (#3894) 
* flex: create variant +lex that creates symlinks for lex and libl.{a,so}

* flex: enable variant +lex by default

* flex: use dso_suffix for portability; replace repetitive code with a loop
 2017-05-21 08:33:34 -05:00
Massimiliano Culpo
e4a3295c37 spark: remove whitespaces from run_env variable (#4210) 2017-05-20 23:40:59 -05:00
Michael Kuhn
17b2db0bd2 Fix ncview with netcdf+mpi (#4305) 
ncview has to be compiled using the same compiler as netcdf.
 2017-05-20 20:59:15 -05:00
Michael Kuhn
c741cd900b magics fixes for versions > 2.29.x (#4302) 2017-05-20 09:40:10 -05:00
Erik Schnetter
a32f8c33b0 julia: New version 0.5.2 (#4259) 2017-05-19 17:32:40 -05:00
Erik Schnetter
4b075de9de hwloc: new version (#4272) 2017-05-19 17:32:16 -05:00
Erik Schnetter
eb001e4d5d hpx5: new version (#4273) 2017-05-19 17:31:53 -05:00
Erik Schnetter
ff6ebe30e0 cmake: new version (#4274) 2017-05-19 17:31:20 -05:00
Michael Kuhn
a62bbb6ed8 gobject-introspection depends on pkg-build (#4301) 2017-05-19 17:30:54 -05:00
Adam Moody
efbcdafd30 Mpifileutils (#4283) 
* adding mpifileutils

* mpifileutils: add +lustre variant

* mpifileutils: add variant for xattr

* mpifileutils: update to AutotoolsPackage

* mpifileutils: simplify and eliminate redundant make

* mpifileutils: drop unnecessary comments
 2017-05-19 17:09:21 -05:00
Michael Kuhn
571a42d614 Fix gcc not finding zlib (#4291) 2017-05-19 12:03:56 -05:00
Douglas Duckworth
8b47fe5a78 added R 3.4.0, again (#4260) (#4294) 2017-05-19 11:55:48 -05:00
George Hartzell
18c7e96624 Fix boost@:1.56.0%gcc@:5 (#4295) 
I need boost@1.54.0 for bcl2fastq2.  I tested bcl2fastq2 using the
system compiler (gcc@4.8.5).  My full build uses a spack-build
gcc@5.4.0.

boost@1.54.0 won't build.  I found the answer
[here](https://github.com/hashdist/hashstack/issues/802) with the
details in [this upstream/boost
ticket](https://svn.boost.org/trac/boost/ticket/10125).

I've confirmed that these combo's build:

boost version| compiler
------------ | ------------------
boost@1.54.0 | gcc@4.8.5 (system)
boost@1.54.0 | gcc@5.4.0 (Spack)
boost@1.64.0 | gcc@5.5.0 (system)
 2017-05-19 11:55:21 -05:00
Tom Merrick
0bff9c1eb1 Add r-rmpfr and r-gmp to R (#4287) 
* Add mpi support to R

* Add multiple precision math routines to R

* Updated the URL to match the version

* Remove duplicate packages
 2017-05-19 09:59:35 -05:00
George Hartzell
be356cf707 Add info for libxml2@2.7.8 (#4290) 
bcl2fastq2 needs this older version.
 2017-05-18 19:02:03 -05:00
kothah
153a63de62 added new version 7.900.1 (#4292) 
added new md5
 2017-05-18 19:01:40 -05:00
Douglas Duckworth
f72cd79ad1 add mpi support to meme (#4265) 
* added openmpi support to meme

* openmpi is a link dependency which leverages r_path

* openmpi support now the default - meme does not have configure argument for mpi - if it's found then it's used

* added serial option and set mpi to not be default

* modified meme
 2017-05-18 15:37:47 -05:00
Tom Merrick
55fc50fa5b Remove duplicate packages 2017-05-18 15:19:18 -05:00
Tom Merrick
fcd3b90326 Merge remote branch 'origin/develop' into develop 2017-05-18 13:47:50 -05:00
Adam J. Stewart
04ccb8f774 Add old version of ROOT 5 (#4288) 2017-05-18 13:22:09 -05:00
Adam J. Stewart
fa90a65d09 Fix spec['python'].home (#4228) 2017-05-18 12:12:08 -05:00
Tom Merrick
5486d021d6 Add mpi support to R (#4286) 2017-05-18 11:24:40 -05:00
Tom Merrick
27a284be90 Updated the URL to match the version 2017-05-18 11:14:51 -05:00
Patrick Gartung
a29921b995 Add the gnupg package and missing dependencies. Update versions of ex… (#4281) 
* Add the gnupg package and missing dependencies. Update versions of existing dependencies.

* this ended up in the wrong repo

* put versions back, remove uneeded function

* OK ;)

* autopep8

* typo on npth line

* whitespace
 2017-05-18 10:11:27 -05:00
Adam J. Stewart
48588cb1d8 Add a new package for Open Babel (#4256) 
* Add a new package for Open Babel

* Add post-installation tests, stolen from the fine folks at Homebrew

* Add patch to fix Python 3.6 support

* Add a more complete patch to get Python 3.6 support working

* Add patch to convert tabs to spaces in test script

testpdbformat.py contains mixed tabs and spaces
causing the unit tests to fail. With this patch,
all tests pass with flying colors.
 2017-05-18 10:06:44 -05:00
Tom Merrick
13508a2e6b Add multiple precision math routines to R 2017-05-18 08:12:13 -05:00
Tom Merrick
a0388f0f03 Add mpi support to R 2017-05-18 07:51:20 -05:00
Erik Schnetter
48eec5fc0f benchmark: New package for the Google Benchmark library (#4194) 
* benchmark: New package

* benchmark: Remove empty function
 2017-05-17 20:58:32 -05:00
George Hartzell
8eeb63e78e Add info for miniconda[23]@4.3.14 (#4263) 2017-05-17 20:57:48 -05:00
George Hartzell
daaa37c1ff Package for bcl2fastq2 (updates libxslt) (#4234) 
* Add v1.1.26 and make crypto a variant

I need 1.1.26 for bcl2fastq2.

I also need to build it without crypto support.

* Initial support for bcl2fastq2

* Clean up commentary, messages, names

No substantial changes intended, just cleanup.

* fix flake8 and extra import

* The masked grammarian strikes again...

* Be normal (messages don't end in periods)

* When +crypto, add --with-crypto

Add `--with-crypto` to configure args when user hasn't explicitly set
`~crypto`.

* self.spec.satisfies is unsatisfying, in is in instead

See #4135, self.spec.satisfies has issues.  @adamjstewart suggests
simply using in.
 2017-05-17 20:57:23 -05:00
Todd Gamblin
32c570913d Move doc dependencies to requirements.txt for readthedocs (#4280) 
* Move doc dependencies to requirements.txt for readthedocs

* Move sphinx to doc requirements.
 2017-05-17 20:45:03 -05:00
Adam J. Stewart
5b527e2c14 Add a new package for sphinxcontrib-programoutput (#4267) 2017-05-17 19:51:15 -05:00
Adam J. Stewart
bb451f967c Add latest version of matplotlib (#4279) 2017-05-17 19:50:50 -05:00
Adam J. Stewart
96560cc11f Add latest version of Sphinx (#4264) 
* Add latest version of Sphinx

* Flake8 fix
 2017-05-17 18:07:10 -05:00