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Author SHA1 Message Date
Sergey Kosukhin
bd92cc0a1a Package 'openjpeg': set INSTALL_NAME_DIR on MacOS for old versions. (#6603) 2017-12-08 13:36:20 +01:00
Paschalis Korosoglou
1bdea98978 r-rhtslib: added build dependency on autoconf (#6627) 2017-12-08 11:18:25 +01:00
Eric
1c72a5da3a py-cogent: Create new package (#6624) 2017-12-08 10:38:37 +01:00
Denis Davydov
23d56a75ab dealii: update boost dependency (#6586) 
(i) blacklst 1.65.0 due to issues on Ubuntu with gcc 5.4.0
(ii) add a patch for 1.65.1 to fix serialization
(iii) simplify boost's depends_on()
 2017-12-08 10:37:54 +01:00
lingnanyuan
96476a32e5 py-htseq: Create new package. (#6623) 2017-12-08 10:36:57 +01:00
Brian Van Essen
20fc7d56d7 Candle benchmarks update (#6619) 
Added a dependency on HDF5 support for the CANDLE benchmarks.
 2017-12-08 10:34:49 +01:00
Benedikt Riedel
df184c707a Adding openssl dependency to xrootd. Closes #6601 (#6618) 2017-12-08 10:33:08 +01:00
nshtg
17692d6c05 Update vim to 8.0.1376 (#6599) 2017-12-08 10:29:50 +01:00
Eric
6f34c68aff subread: Add version 1.6.0 (#6615) 2017-12-08 10:26:18 +01:00
Denis Davydov
26e109027b qrupdate: fix blas/lapack and compilation of macOS (#6614) 2017-12-08 10:24:44 +01:00
Eric
62d5bb41a8 py-reportlab: Create new package (#6612) 2017-12-08 10:22:46 +01:00
nshtg
636ed371d8 Update fish to 2.7.0 (#6608) 2017-12-08 10:15:40 +01:00
Eric
91eca9143e bedtools2: Add version 2.27.0 (#6606) 2017-12-08 10:13:13 +01:00
Kelly (KT) Thompson
147a12dd06 Provide a patch to allow hdf5@1.10.1 to build with intel/18.0.1. (#6583) 
This is known issue.  See:

https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
 2017-12-08 09:55:06 +01:00
Sergey Kosukhin
a593553d48 Update for 'eccodes'. (#6604) 2017-12-08 09:34:37 +01:00
Sergey Kosukhin
a110a86ad6 Update for 'grib-api'. (#6605) 2017-12-08 09:33:30 +01:00
Jon Rood
69e76a0a89 Update openfast package to explicity pass MPI implementation during cmake configure. (#6590) 2017-12-08 09:09:35 +01:00
Axel Huebl
f49c186f4f wxWidgets: Fix builds (#6560) 
- depends on GTK+ with X enabled
  (btw, non-X backends are deprecated/removed in GTK+)
- patch for 3.0.1-3.0.2: missing include caused multiple
  `error: call of overloaded ‘abs(XYPOSITION)’ is ambiguous`
  (seen in GCC 6.3.0); fixed in 3.0.3+
 2017-12-07 08:33:08 +01:00
Massimiliano Culpo
05b10ce967 config.py: fixed comments that refer to variables following them (#6585) 
According to the documentation here:

  http://www.sphinx-doc.org/en/stable/ext/autodoc.html

"For module data members and class attributes, documentation can either
be put into a comment with special formatting (using a #: to start the
comment instead of just #), or in a docstring after the definition."
 2017-12-07 08:09:53 +01:00
lingnanyuan
3a4329c77d r-pathview: Create new package. (#6582) 2017-12-06 18:29:45 -07:00
lingnanyuan
c2ea795b08 r-kegggraph: Create new package. (#6580) 2017-12-06 18:29:22 -07:00
lingnanyuan
96c95db793 r-org-hs-eg-db: Create new package. (#6581) 2017-12-06 18:29:04 -07:00
Sergey Kosukhin
9a4dd413bb Package 'libszip': update checksum and list_depth. (#6587) 2017-12-06 18:28:11 -07:00
Sergey Kosukhin
bcb1630e39 CMAKE_INSTALL_RPATH is semicolon-separated. (#6577) 2017-12-06 08:07:11 +01:00
Eric
24d60a95c0 picard: Add version 2.16.0 (#6579) 2017-12-06 08:04:06 +01:00
Audrey Thoma
a97824df98 mrbayes: url now points to github + removed the deprecated sourceforge url (#6578) 2017-12-06 07:58:08 +01:00
Jon Rood
5c43090ceb Update CGNS and add CGNS capability to Trilinos (#6568) 
* Update CGNS to be able to be used in Trilinos.

* Updating Trilinos to be able to use CGNS.

* Fixing wrong cmake defines in trilinos for enabling cgns and cleaning up cgns package.

* Changing cgns parallel variant to mpi. Removing explicit dependence on parallel-netcdf in trilinos.
 2017-12-05 14:33:36 -07:00
nshtg
01ba69c635 Update gnupg to 2.2.3 (#6573) 
Updated dependencies:

* libassuan 2.4.5
* libgcrypt 1.8.1
* npth 1.5
 2017-12-05 14:29:20 -07:00
Axel Huebl
9e64fa53ed Add Maintainer (#6575) 
Add myself as maintainer to the packages we contributed
and/or maintain the mainline from.
 2017-12-05 14:27:56 -07:00
Jon Rood
67d7f3fc03 Add opennurbs package (#6570) 
* Adding OpenNurbs package.

* Fixing flake8 error.

* Removing unused os import from opennurbs.
 2017-12-05 10:33:55 -07:00
Axel Huebl
5a908a1c8a ADIOS 1.13.0: LZ4 & blosc support (#6572) 
Add additional transform libraries to ADIOS.
Also modifies existing transforms to the versions they were
introduced (otherwise this was resulting in unknown configure flags).
 2017-12-05 15:28:44 +01:00
Axel Huebl
e47d89a2ab ADIOS 1.13.0: Newer SZ Versions (#6561) 
The latest release of ADIOS needs a newer version of SZ due to an upstream library naming change.
 2017-12-05 12:50:22 +01:00
Axel Huebl
09e68c5c8a c-blosc: 1.12.1 (#6571) 
Adds a newer release of c-blosc, adds the new flags for external library builds, adds missing dependencies.
 2017-12-05 12:49:22 +01:00
Sergey Kosukhin
90c7bc7a24 OpenJPEG: all version tuples have the same length. (#6526) 2017-12-04 17:44:53 -07:00
Paschalis Korosoglou
b2c6306b94 Added package r version 3.4.3 (#6565) 2017-12-04 17:39:34 -07:00
Axel Huebl
9ad3b1a747 libpng: CPPFLAGS for -I (#6563) 
Recent versions of `libpng` (e.g. 1.6.34) warn/abort that includes
for `zlib` need to be passed properly via `CPPFLAGS`. This fixes it.
 2017-12-04 15:29:35 -07:00
Eric
6968777af7 bamtools: Add version 2.5.0 (#6553) 2017-12-04 10:38:30 -07:00
Denis Davydov
e9c66a76f0 dealii: add scalapack and various cleanups (#6552) 2017-12-04 08:02:05 +01:00
Chien-Chang Feng
f564e02301 py-h5py: fixed a typo in the name of a dependency (#6540) 2017-12-04 07:50:35 +01:00
Benedikt Riedel
6887107775 Adding zlib dependence to xrootd to resolve #6545 (#6550) 2017-12-03 16:22:44 -07:00
Eric
10ad2bc1bf py-multiqc: Add version 1.3 (#6554) 2017-12-03 16:21:27 -07:00
Yifan Zhu
1e702bfab0 r-fftwtools: new package (#6532) 2017-12-03 16:20:32 -07:00
Paschalis Korosoglou
79751729c9 Rename variant static to shared (#6543) 2017-12-03 16:19:32 -07:00
Denis Davydov
13dade60dd gcc: remove all variant (#5283) 2017-12-03 10:19:55 +01:00
Nils Deppe
07fcd0d115 Add Kvasir MPL (#6529) 2017-12-02 16:02:43 -07:00
Eric
6918ee3767 salmon: Add version 0.9.1 (#6516) 2017-12-02 12:45:10 -07:00
sknigh
80048ae4a9 Paraview expects qt to have opengl (#6520) 2017-12-01 13:46:39 -07:00
Patrick Gartung
f6c99d7beb Buildcache: relocate fixes (#6512) 
* Updated function which checks if a binary file needs relocation.
  Previously this was incorrectly identifying ELF binaries as symbolic
  links (so they were being excluded from relocation). Added test to
  check that ELF binaries are not considered symlinks.

* relocate_text was not replacing paths in text files. Added test to
  check that text files are relocated properly (i.e. paths in the file
  are converted to the new prefix).

* Exclude backup files created by filter_file when installing from
  binary cache.

* Update write_buildinfo_file method signature to distinguish between
  the spec prefix and the working directory for the binary cache
  package.
 2017-12-01 11:15:16 -08:00
Axel Huebl
d6863a2940 ADIOS: 1.13.0 (#6539) 
New release of ADIOS: 1.13.0.
 2017-12-01 11:09:37 -07:00
Stephen Hudson
d5c96dbd94 Add new package py-libensemble (#6525) 2017-12-01 11:01:08 -07:00