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Author SHA1 Message Date
Denis Davydov
e623bbb679 suite-sparse: support 64bit BLAS (#6767) 
* suite-sparse: support 64bit BLAS

* use double quotes instead of escaped quotes
 2018-01-03 09:58:19 -06:00
stefanosoffia
2ed914aa1b Flex v2.6.4 conflicts with gcc@7.2.0 (#6819) 2018-01-03 09:46:57 -06:00
Douglas Duckworth
d466d8f3d3 singularity - added master branch (#6631) 
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch

* renamed to develop

* added master branch properly
 2018-01-02 21:47:21 -06:00
Axel Huebl
5d2f752c1b New Package: py-adios (#5686) 
The ADIOS1 numpy bindings depend on an installed, fully loaded
ADIOS C library + its config tools to build properly.
 2018-01-02 21:37:59 -06:00
Brian Van Essen
3c63710532 Intel mkl dnn (#6268) 
* Added a package for the MDAnalysis toolkit.

* Added a package for the Intel MKL-DNN project.

* Fixed flake8 errors.

* Fixed Flake8
 2018-01-02 21:27:34 -06:00
Eric
d2c3b3884b rsem: update version 1.3.0 md5sum (#6650) 2018-01-02 21:15:40 -06:00
Michael Kuron
2c5c7a37cb atom-dft: new package plus dependencies (#6653) 
* atom-dft: new package plus dependencies

* Indentation fix

* Use the compiler wrappers

* Pass variables instead of using FileFilter
 2018-01-02 20:32:37 -06:00
Jimmy Tang
ea6b6ef1ff Install all the cli tools from all the sub-directories (#6705) 
* Install all the cli tools from all the sub-directories

* Satisfy pep8
 2018-01-02 20:14:39 -06:00
Feiyi Wang
8ed1c84539 py-lrudict: a LRU-based cache dictionary (#6734) 
* add py-lrudict

* style fix

* style fix: add blank lines
 2018-01-02 20:10:49 -06:00
Feiyi Wang
8221265c3c py-scandir: a better directory iterator, backport to 2.7 (#6739) 2018-01-02 20:08:58 -06:00
Levi Baber
59cd2db8f3 gatk: boilerplate cleanup (#6744) 2018-01-02 20:05:04 -06:00
Denis Davydov
4b5fe75bc3 add OctavePackage (#6746) 
* add OctavePackage

1. remove import CudaPackage which is not needed anymore
2. mention CudaPackage and OctavePackage in packaging guide
3. adjust OctavePackageTemplate
4. add clue file for Octave build
5. sanity check on self.prefix

* use setup_environment
 2018-01-02 20:03:27 -06:00
Feiyi Wang
fd6b9ac3af py-xattr: a python interface to access extended file attribute (#6747) 
* py-xattr: a python interface to access extended file attribute

* py-xattr: style fix
 2018-01-02 20:02:03 -06:00
Brian Van Essen
a92268d62a Lbann update (#6751) 
* Added a package for the MDAnalysis toolkit.

* Updated the LBANN recipe to use the revised cmake environment being
rolled out.

* Flake8 errors
 2018-01-02 20:01:23 -06:00
Denis Davydov
3d257e8280 likwid: add stable 4.3.0 (#6761) 2018-01-02 19:59:14 -06:00
Denis Davydov
cc74da5aab mesa: disable binutils on macOS (#6763) 2018-01-02 19:58:38 -06:00
Levi Baber
353870fe50 jags: lapack fix (#6764) 
* jags: fixing openblas thows a lapack error when compiling. atlas works. other lapack providers may work. also adding tags

* changing blas/lapack reference

* removing openblas conflict

* jags: whitespace cleanup for flake8
 2018-01-02 19:57:54 -06:00
Milton Woods
6922ea5889 Esmf fixes for Cray, OSX and mpich (#6768) 
* esmf: put .mod files in the spack compiler search path

* esmf: allow building with Cray mpi

* esmf: create run-path dependent libraries on osx

* esmf: link fortran interface libraries when building with mpich
 2018-01-02 19:43:55 -06:00
Jon Rood
e1e24ff80e Adding option to build Nalu with Hypre support. (#6782) 2018-01-02 19:42:47 -06:00
peetsv
fef93d2221 perl-xml-libxml: adding perl module (#6783) 
* perl-xml-libxml: adding perl module

* line length change
 2018-01-02 19:42:09 -06:00
Sinan
7f319b9f84 create perl-file-which package (#6800) 
* create perl-file-which package

* trivial edits for package.py so

trivial edits for package.py so that flake8 will not complain
 2018-01-02 19:36:59 -06:00
stefanosoffia
2aaba189ed Updated 'nginx' from v1.12.0 to v1.13.8. (#6810) 
This fixes build issues with most recent gcc versions.
See issue #6252.
 2018-01-02 19:29:47 -06:00
Eric
958abe5b29 py-pyani: Create new package (#6811) 2018-01-02 19:27:42 -06:00
Eric
7db7b5b596 MinCED: Create new package (#6815) 2018-01-02 19:25:08 -06:00
Levi Baber
08ea9808c6 adding specific version url for augustus 3.3 due to old folder structure (#6813) 2018-01-02 19:24:28 -06:00
Jon Rood
285538a78d Tioga package: Explicitly list MPI compilers for Cmake (#6741) 2018-01-02 13:14:22 -08:00
Jon Rood
2812644ed7 paraview package: Explicitly specify MPI compilers in Cmake (#6738) 2018-01-02 13:06:25 -08:00
Milton Woods
5dd5dc01c2 new package: Pfunit: unit testing framework for Fortran (#6795) 2018-01-02 12:18:08 -08:00
Eric
e483f9297a new package: DIAMOND (#6793) 2018-01-02 12:03:45 -08:00
Eric
8271f0e271 new package: tantan (#6792) 2018-01-02 12:00:13 -08:00
Adam J. Stewart
b10098dc53 Cython only needed for develop version of mpi4py (#6780) 2018-01-02 11:34:24 -08:00
Eric
9ac9017589 new package: py-rseqc (#6773) 2018-01-02 11:10:55 -08:00
Eric
e8b1e79fbf package py-biopython: remove py-mx dependency (#6772) 2018-01-02 10:59:21 -08:00
Eric
caa39d08d4 package r-rcurl: boilerplate cleanup (#6771) 2018-01-02 10:58:03 -08:00
Eric
c3b003e698 bamtools: Add version 2.5.1 (#6770) 2018-01-02 10:55:07 -08:00
Axel Huebl
da93c9b870 Add: lines-are-beautiful (#6784) 
Adds the C++ File API library "lines-are-beautiful" for the
reMarkable e-ink tablet.
 2017-12-30 12:29:27 -08:00
Nichols A. Romero
24743b7e5a QMCPACK package: update blas/lapack detection (#6753) 
* Fix detection of blas and lapack: provide libraries/includes as
  arguments to CMake rather than using CMake's auto-detection.
  This includes a patch to QMCPACK's CMake files to refer to
  Spack-built blas/lapack implementations. This also includes
  special-case logic for the intel-mkl implementation of blas/lapack

* Break up unit tests and short tests. Only hard failure if the unit
  tests fail, if short tests fail issue a warning only.

* Add QMCPACK 3.3.0, get rid of 3.0.0
 2017-12-22 16:47:49 -08:00
Denis Davydov
f764ac4573 dealii: support 64bit BLAS (#6758) 2017-12-22 15:55:04 +01:00
Andrey Prokopenko
937f68c359 clang,flang: update CC, CXX environment in installation module (#6737) 2017-12-22 07:32:10 +01:00
peetsv
d1786779c4 gmap-gsnap: adding version 2014_12_28 (#6720) 2017-12-22 06:56:58 +01:00
Levi Baber
f2e061debf Feature/fasttree (#6227) 
* fasttree: new package

* fasttree: better version handling

* fixing line length for flake8
 2017-12-20 19:10:24 -08:00
Mark Olesen
ef2e51571d ENH: better handling of mpich for openfoam packages 
- define MPICH_SKIP_MPICXX, link libmpich instead of libmpi
  (as per disussion in PR #4990)

ENH: more flexible editing/patching of openfoam env files

CONFIG: comment out requirement for openmpi+thread_multiple

- was originally slated for the 1712 release and beyond, but there are
  reportedly unstable version/network combinations.
  Leave as comment for future reference, since it may be arise again.

STYLE: renamed openfoam-site.patch as 1706-site.patch (and reformatted)

- to preserve against impending changes in the layout of
  config.{csh,sh}/settings
 2017-12-20 11:32:33 -08:00
Mark Olesen
235c3c1025 ENH: improved openfoam module creation (issue #4942) 
- post-install module settings for openfoam-com and foam-extend.
 2017-12-20 11:32:33 -08:00
Eric
6ea4614dbd picard: Add version 2.17.0 (#6729) 2017-12-20 13:28:37 +01:00
Denis Davydov
ea5f8c7382 octave: add optim and struct packages (#6733) 2017-12-20 13:27:50 +01:00
Gregory Lee
241ea77229 sqlite package: apply B0 patch to additional versions (#6728) 2017-12-19 11:06:39 -08:00
Denis Davydov
0ef741d291 slepc: add 3.8.2 (#6724) 2017-12-19 15:40:30 +01:00
Denis Davydov
e462d39afe intel-tbb: add 2018.2 (#6725) 2017-12-19 15:39:42 +01:00
Denis Davydov
98f220b304 hypre: add 2.13.0 (#6726) 2017-12-19 15:39:27 +01:00
Denis Davydov
599094abbd suite-sparse: add 5.1.0 (#6727) 2017-12-19 15:39:12 +01:00
Jack Morrison
720ad57bcd Added GDB verison 8.0 (#6704) 2017-12-19 09:54:18 +01:00
peetsv
d0a10edb67 nextflow: adding version 0.21.0 (#6722) 2017-12-19 09:07:33 +01:00
Peter Doak
d4c84be91b Emacs: added gnutls variant (tested on Centos 7) (#6711) 2017-12-19 08:36:54 +01:00
Denis Davydov
69f959ec0b gmsh: add 3.0.6 (#6718) 2017-12-19 08:31:23 +01:00
junkudo
d69d692203 CoinHSL : Prevent CoinHSL from building in parallel (#6715) 
CoinHSL does not seem to be able to be built in parallel. This commit forces serial compilation.
 2017-12-19 08:30:39 +01:00
Denis Davydov
548c225d45 dealii: add GMSH, add CMAKE_FIND_APPBUNDLE to CMakePackage (#6723) 
* dealii: add GMSH dependency

* CMakePackage: add CMAKE_FIND_APPBUNDLE to prevent picking up binaries from /Applications
 2017-12-19 08:28:55 +01:00
peetsv
e8de22ce46 lftp: adding version 4.6.4 (#6721) 2017-12-19 08:19:33 +01:00
Mark Olesen
b3e9192d18 openfoam-org: new version (#6686) 
Add new version with a patch.
 2017-12-18 19:47:49 -08:00
peetsv
f7a5a27138 IGV: new package (#6710) 2017-12-18 19:37:09 -08:00
Benedikt Riedel
36fa574779 globus-toolkit: add version and openssl dependency (#6617) 2017-12-18 15:23:56 -08:00
Douglas Duckworth
d3519af7de relion - added new stable version 2.1 (#6706) 2017-12-18 10:38:20 -08:00
healther
0cff0fba73 fix post install method for py3 in mercurial (#6497) 
* fix post install method for py3 in mercurial

* Update package.py

* Update package.py

* use print_str instead of manual print detection

* Update package.py

* use only depends_on

* Update package.py

* Update package.py

State py3 compatibility for @4.3: according to setup.py from the 4.3.tar.gz from pypi
 2017-12-17 12:00:58 -06:00
Sergey Kosukhin
576ef5e2b3 Package 'cdo': get rid of unnecessary dependency on MPI C++ library. (#6632) 2017-12-16 19:48:56 -07:00
nshtg
2a639097b0 Add new package signify (#6645) 
OpenBSD tool to sign and verify signatures on files.

See https://github.com/aperezdc/signify
 2017-12-16 19:47:59 -07:00
Eric
7d800a0fc2 breseq: Create new package (#6648) 2017-12-16 19:47:11 -07:00
fpruvost
6c81cf1a78 build lapacke with tmg (#6654) 2017-12-16 19:43:46 -07:00
David Orman
7b8d889d31 bwa: added version 0.7.16a and checksum (#6658) 2017-12-16 19:43:02 -07:00
Jack Morrison
d4cc1ac86b Hadoop: Replace broken url (#6671) 2017-12-16 19:42:03 -07:00
David Böhme
3467c207c8 Caliper update, add version 1.6.0 (#6680) 2017-12-16 19:39:52 -07:00
Eric
dac09dd5fb py-bx-python: Create new package (#6672) 2017-12-16 19:38:59 -07:00
Eric
d08dc0c019 py-tetoolkit: Create new package (#6673) 2017-12-16 19:38:36 -07:00
Eric
d3545ed1b3 py-pandas: add versions 0.19.2 and 0.21.1 (#6687) 2017-12-16 19:38:02 -07:00
Paschalis Korosoglou
a69cfd5f78 Add petsc version 3.8.3 (#6688) 2017-12-16 19:37:35 -07:00
Paschalis Korosoglou
61dbd3182d Add clanguage variant for petsc (#6689) 2017-12-16 19:37:20 -07:00
Eric
87420dccee bedtools2: Add version 2.27.1 (#6693) 2017-12-16 19:36:35 -07:00
peetsv
5d0e7abcc5 MetaSV: adding new package (#6691) 2017-12-16 19:36:11 -07:00
Eric
5539c94e67 PANDAseq: Create new package (#6694) 2017-12-16 19:35:48 -07:00
Eric
554d4045fa DeNovoGear: Create new package (#6699) 2017-12-16 19:34:53 -07:00
lingnanyuan
34cf796b54 mefit: Create new package. (#6700) 2017-12-16 19:34:30 -07:00
Denis Davydov
f78418d8bb moltemplate: add new package (#6702) 2017-12-16 19:33:28 -07:00
David Orman
176b518d4b new package: gatk (#6674) 2017-12-15 11:00:55 -08:00
Jon Rood
7369ba21bf new package: Percept (#6636) 
This also adds the 'exception' boost library to the set of default
libraries built by boost.
 2017-12-14 18:11:47 -08:00
Douglas Duckworth
1aed3f7c01 added breakdancer (#6319) 2017-12-14 14:43:32 -07:00
Massimiliano Culpo
6c1fa37e3d
fftw: added version 3.3.7 (#6678) 2017-12-14 21:38:33 +01:00
Jon Rood
b447c2ba51 Add TIOGA package and optional dependency of Nalu on TIOGA (#6638) 2017-12-14 11:46:25 -08:00
Scott Wittenburg
ce832fca59 libharu: Make dependencies on zlib and libpng explicit (#6682) 2017-12-14 08:58:42 +01:00
Douglas Duckworth
5a66065dfa relion: add version and cuda arch variant (#6317) 
Add preferred version 2.0.3. Added beta version. Added conflict with
gcc versions >= 5 when building with cuda@8 (which is currently the
only supported cuda version). Added cuda architecture variant. Added
comment about current lack of cuda@9 support.
 2017-12-13 10:30:38 -08:00
Denis Davydov
c0aa12111b tasmanian: add new package (#6659) 2017-12-13 16:01:51 +01:00
Axel Huebl
836bf65250 CUDA: 9.1 (#6663) 
Add the latest CUDA release, 9.1
 2017-12-13 14:43:40 +01:00
peetsv
2e4c9e47a8 py-pysam: adding old version 0.7.7 (#6675) 2017-12-13 09:01:45 +01:00
Eric
5fa9e61321 SPAdes: add version 3.11.1 (#6668) 2017-12-13 08:57:29 +01:00
David Orman
c5cb8ae159 picard: added version 2.13.2 (#6669) 2017-12-13 08:57:06 +01:00
Audrey Thoma
45784af7f2 new packages: biopieces and dependencies (#6478) 
This also adds the tcl, tk, and libx11 dependencies to ruby. All other
changes are new packages.
 2017-12-12 18:35:13 -08:00
Christoph Junghans
27be66420a
laghos: inject CXX (#6664) 2017-12-12 17:26:02 -07:00
Christoph Junghans
e80a27d713
swfft: inject CC/CXX (#6666) 2017-12-12 17:25:48 -07:00
Satish Balay
80284617a5 xsdk: update xsdk@develop to use sundials, plasma, magma (#6649) 
Also update xsdk@0.3.0 to use a fixed version of magma
 2017-12-12 09:31:08 -08:00
nshtg
e831ecbf3a Add new package minisign (#6644) 
A dead simple tool to sign files and verify signatures.

See https://jedisct1.github.io/minisign
 2017-12-11 17:27:40 -07:00
nshtg
45e8e4b4fb libsodium: Update to 1.0.15 (#6643) 2017-12-11 17:27:09 -07:00
nshtg
25aa21a7a7 git: Update to 2.15.1 (#6642) 2017-12-11 17:26:53 -07:00
nshtg
74938f58d2 openssl: Update to 1.0.2n (#6641) 
From 07.12.2017, fixes CVE-2017-3737
 2017-12-11 17:26:37 -07:00
Brian Van Essen
6fec473e9e Py h5py update (#6635) 2017-12-11 17:26:13 -07:00
健美猫
e19aa80734 intel-parallel-studio: restrict patch to versions > 2016 (#6523) 
Fixes #6522

Patch psxevars.sh and psxevars.csh only when year > 2016.
pxevars.csh does not exist for versions before 2017. psxevars.sh
does not appear to require this patch for versions before 2017.
 2017-12-11 13:14:24 -08:00
Johann Klähn
e83c3d1b6a bazel: include SPACK_DEBUG_LOG_ID in environment (#6562) 
Fixes #6521.

Bazel's build system filters environment variables, including those
set by Spack for use by its compiler wrapper. This updates the patch
to include the SPACK_DEBUG_LOG_ID variable added in #5837.
 2017-12-11 10:34:06 -08:00
Satish Balay
53b2ec356b disable plasma in xsdk 0.3.0 (#6621) 2017-12-10 17:51:54 -08:00
Adam J. Stewart
f41a263a28 Fix reference to self.versions in neovim package (#6639) 2017-12-10 21:43:49 +01:00
Cyrus Harrison
95a384f051 updates to conduit and ascent packages (new PR) (#6584) 
* optional path to use spacks py-site-pkgs, install host-cfg for provenance

* add more comments and address review requests

* only use st-pkgs-dir when +python

* ascent does not need doxygen

* capture mpiexec if it exists

* added missing import

* flake8 fix

* default adios variant to False

* ascent develop now reqs conduit master

* optional path to use spacks py-site-pkgs, install host-cfg for provenance

* add more comments and address review requests

* only use st-pkgs-dir when +python

* ascent does not need doxygen

* capture mpiexec if it exists

* added missing import

* flake8 fix

* default adios variant to False

* ascent develop now reqs conduit master

* conduit: use hdf5 1.8 for wider output compat
 2017-12-08 13:43:12 -08:00
Chris Green
e279299b9b Relax restriction on lua version. (#5886) 2017-12-08 20:52:00 +01:00
Thilina Rathnayake
c1bc1be2a7 Add NekCEM package to spack (#6509) 2017-12-08 10:30:42 -07:00
Thilina Rathnayake
d6db532095 Update the Nekbone package (#6508) 2017-12-08 10:29:58 -07:00
healther
4c02e7e9f4 add restriction to py-setuptools dependency on py-flake8 (#6589) 2017-12-08 10:22:52 -07:00
Eric
bb8e7ee023 Perl-statistics-descriptive: Create new package (#6588) 2017-12-08 10:22:16 -07:00
Axel Huebl
5bf19a9d84 Fix AstroPy: Missing Markupsafe (#6630) 
`py-markupsafe` was missing during `spack install` as a build error.
 2017-12-08 10:21:46 -07:00
Axel Huebl
353ea07040 Add: Py-Plotly (#6628) 
* Add: Py-Plotly

The requirements of py-plotlit are rather strict fixed to specific
versions, so I did not add an "upper versions" `:` to the constrains.
See
  https://github.com/plotly/plotly.py/blob/master/requirements.txt

* Py-Requests, Py-Six, Py-Pytz: Older Versions

Add two older versions of requests, pytz and six for plotly.
 2017-12-08 10:21:28 -07:00
Paschalis Korosoglou
5e8139cbd1 Fix in download url for package libaio (#6616) 2017-12-08 10:20:14 -07:00
nshtg
e283a79da6 Update zsh to 5.4.2 (#6609) 2017-12-08 10:19:40 -07:00
lingnanyuan
3474dd5d40 r-tidycensus: Create new package. (#6595) 2017-12-08 10:18:45 -07:00
lingnanyuan
cc20ad0eec r-rgdal: Create new package. (#6593) 2017-12-08 10:18:29 -07:00
lingnanyuan
85c4224474 r-tigris: Create new package. (#6591) 2017-12-08 10:18:11 -07:00
nshtg
173236dacf Update openSSL to 1.0.2m/1.1.0g (#6596) 2017-12-08 10:13:58 -07:00
nshtg
fd764b9946 Update openSSH to 7.6p1 (#6598) 2017-12-08 10:13:41 -07:00
nshtg
1954075091 Update tmux to 2.6 (#6597) 2017-12-08 10:13:22 -07:00
Tzanio Kolev
2343e5185d Updated hash for v1.0 tag of Laghos (#6626) 2017-12-08 10:12:33 -07:00
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
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
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
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
Eric
fa32f8f914 py-dendropy: Create new package (#6528) 2017-12-01 11:00:45 -07:00
Paschalis Korosoglou
bd94be818a Added variant static for hwloc (#6538) 2017-12-01 06:25:23 -07:00
Yifan Zhu
e0264404b6 r-udunits2: new package r-udunits2 (#6533) 2017-12-01 11:16:35 +01:00
Yifan Zhu
4a55f81051 r-units: new package (#6531) 2017-12-01 05:26:05 +01:00
Adam J. Stewart
3dafbe901a Fix CGAL checksum and switch to more stable URL (#6511) 2017-11-30 09:18:54 +01:00
healther
130c56dbaa add package py-lazy-object-proxy (#6489) 2017-11-30 09:17:28 +01:00
lingnanyuan
5382279fa6 r-biomformat: Create new package. (#6517) 2017-11-30 09:14:12 +01:00
lingnanyuan
f9c820c39f r-phyloseq: Create new package. (#6518) 2017-11-30 09:13:31 +01:00
Yifan Zhu
86fbcc7140 r-nanotime: new package (#6519) 2017-11-30 09:12:58 +01:00
Michael Bentley
a097524281 Flit package (#6260) 
Add initial build support for version 2.0-alpha.1
 2017-11-30 09:05:40 +01:00
Stephen Hudson
02371d2ace Add new package nlopt (#6499) 2017-11-29 10:27:08 +01:00
healther
cc5d5295bd add missing build dependency to py-pytest-runner (#6490) 2017-11-28 16:52:18 -07:00
Yan Grange
b5f3ecf3fa Update globus package version and hash (#6482) 2017-11-28 16:51:35 -07:00
Michael Kuhn
9adcb0b4b1 libmongoc: Fix pkg-config file not containing snappy and zlib paths (#6467) 2017-11-28 16:47:12 -07:00
healther
f7fda19f5d remove breaking version and cleanup of dependencies (#6494) 2017-11-28 16:46:23 -07:00
healther
8013996661 add conflicts to py-enum34 (#6496) 2017-11-28 16:45:08 -07:00
healther
2190ae43a5 Fix astroid dependency and mark broken version (#6493) 2017-11-28 16:43:43 -07:00
healther
cab07d2562 add package py-editdistance (#6492) 2017-11-28 16:43:00 -07:00
healther
82adc403ad add package py-isort (#6491) 2017-11-28 16:42:47 -07:00
healther
64b121fa87 add package: py-backports-functools-lru-cache (#6488) 2017-11-28 13:54:40 -08:00
becker33
acd80b16a8
update scr package for cray (#6407) 
* update scr package for cray

* added info on scr version 1.2.0
 2017-11-28 10:33:45 -08:00
Denis Davydov
ddb55c2b26 py-numpy: add 1.13.3 (#6484) 2017-11-28 13:42:59 +01:00
Denis Davydov
fdb2386ba7 pi-scipy: add 1.0.0 (#6486) 2017-11-28 13:42:27 +01:00
Yifan Zhu
bec8ddcf81 r-classint: created new package (#6481) 2017-11-28 09:29:29 +01:00
Yifan Zhu
5cdf94233b r-rcppcctz: created new package (#6480) 2017-11-28 09:28:42 +01:00
lingnanyuan
8d64e192dc r-topgo: Create new package. (#6479) 2017-11-28 09:27:36 +01:00
Eric
6edd782d39 r-seurat: Create new package (#6477) 2017-11-28 09:27:14 +01:00
Eric
7f43411e59 Adding list_url to several R module packages (#6474) 2017-11-28 09:26:06 +01:00
Yifan Zhu
63a23b93c5 r-cli: new package (#6476) 2017-11-28 09:21:12 +01:00
Satish Balay
cd8da5a441 Xsdk 0.3.0 (#6277) 
* xsdk:  Added MFEM rc package.

* xsdk: add version entry for xsdk-0.3.0-rc1 - and set it as preferred version

* xsdk: remove 'xsdk' from version - recommended by Todd.

Now the usage is:
 'spack install xsdk@0.3.0-rc1'

instead of the previous usage:
 'spack install xsdk@xsdk-0.2.0'

* xsdk: add petsc@3.8.0 as a dependency for xsdk-0.3.0-rc1

* mfem: fix dependency to use the corrected xsdk version

* Updated the mfem version tags.

* mfem: fix merge

* fix flake8 warning

* Modified xSDK scripts

* fixing the default package.yaml

* fix bad revert

* revert changes to superlu-dist so that the 5.2.1 update can be merged

* update xsdk to use superlu-dist-5.2.1

* update alquimia for xsdk

* fix whitespace

* update hypre for xsdk

* update sundials for xsdk

* update sundials for xsdk

* Fix checking for MKL and extend range of GCC versions

* pflotran: update to release branch

* plasma: fix spec -> self.spec

* Changes to enable mfem hooks into hypre, superlu-dist, and petsc.  Sundials hooks may come in the future.

* adding plasma with comment

* Bumped the version of mfem up to handle integration with sundials3.0.0.  Also enabled hypre in sundials.

* Turn on the plasma package definition for testing

* Fix conflict declaration to obey ordering rules

* xsdk: udate superlu-dist dependency to v5.2.2

* plasma: change gcc dependency to workarround potential spack bug #5778

* trilinos: update hdf5 dependency to use 'hdf5+hl'

Without this change - I get the following error [triggered by 161dca6d5 c9810f808 changes]

$ ./bin/spack install trilinos+hdf5
==> Error: An unsatisfiable variant constraint has been detected for spec:

    hdf5@1.10.1%gcc@7~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-fedora27-x86_64

while trying to concretize the partial spec:

    netcdf+mpi
        ^m4
        ^mpich@3.3a2%gcc@7 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-fedora27-x86_64
        ^zlib@1.2.11%gcc@7+optimize+pic+shared arch=linux-fedora27-x86_64

netcdf requires hdf5 variant +hl, but spec asked for ~hl

* plasma: add in -lm dependency per #6046

* update sundials version to 3.0.0

* Add fixes to support Netlib LAPACK

* mfem does not use cmake for builds [anymore] - so remove code corresponding to this dependency.

This enables mfem build on OSX [with xcode/clang compilers]

* mfem: update to v3.3.2-rc4

* add patch for building sundials on mac

* xsdk: enable plasma for gcc-4.9+ - same as what plasma/package.py does.

* magma: Fix for cuda-9.0  as it does not support sm20

nvcc fatal   : Unsupported gpu architecture 'compute_20'

* add in code for 'spack install xsdk+cuda' - which installs magma

* fix flake8 warning

* fix flake8 warnings

* Updated to the latest MFEM RC.

* alquimia: fix to use petsc-3.8.0+ versions

* petsc: update to version 3.8.1

* petsc: add in conflict between petsc-3.8.0 & mkl

* xsdk: update petsc to 3.8.1 to get MKL build fix

* petsc: fix superlu_dist dependency

* petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configured with zlib

* petsc: fix dependency [of zlib to be on hdf5 - and not on petsc]

* petsc: fix pkgconfig error - with incorrect library link order that can break mfem examples with static build

* petsc: use the fact that hdf5/package.py has a hard dependency on zlib [so no need to check for this dependency in code]

recommended-by: @davydden

* petsc: change hdf5 dependency to 'hdf5+hl' as petsc configure is looing for -lhdf5_hl

https://github.com/spack/spack/issues/5846

* plasma: also detect -lgfortran

* update sundials version to 3.1.0

* alquimia: xsdk-0.3.0-rc -> xsdk-0.3.0

* petsc: update to version 3.8.2

Includes pkgconfig fix [for mfem static build failure]

* Revert "petsc: fix pkgconfig error - with incorrect library link order that can break mfem examples with static build"

This reverts commit d1afa8c20d4313fdc42a27e5380573b035b32998.

* xsdk: update to use petsc-3.8.2

* Fixed a problem with MFEM trying to use mpicxx instead of the spack defined compiler.

* Minor changes to the mfem build and pointing at mfem's release branch that is currently undergoing internal testing.

* Enabling shared build for Plasma

* plasma: do not look for libgfortran on cray - spack finds the wrong one from the frontend

'-L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/lib64 -lgfortran'

* Some changes to the mfem package that are in the process of being pulled into spack/develop.

* xsdk: switch from 0.3.0-rc1 to 0.3.0

* fix flake8 warnings

* plasma: extract plasma changes from xsdk-0.3.0

* plasma: cleanup per review
- netlib-lapack: add support for spec['lapack:c'].libs, spec['blas:c'].libs
- add getblaslapacklibs() to eliminate duplicate code in edit() and build_targets()
- eliminate string manipulation of ld_flags

- remove gfortran check (will check later)
- remove build() (will check later)

* netlib-lapack: fix tuple per review

* netlib-lapack: use  spec[lapack:c,fortran]
 2017-11-27 22:08:08 -08:00
peetsv
52f46d2bee ViennaRNA: adding version 2.4.3 + disable swig (#6408) 
* Adding version 2.4.3 to ViennaRNA

* Replaced tab indent with spaces

Flake8 error correction

* no swig for viennarna v2.4.3 only

* correcting version/argument conditional syntax error
 2017-11-27 16:45:43 -07:00
Mark Berrill
e2abebe8a5 Adding new package amp (#6471) 2017-11-27 14:43:03 -07:00
Quinn
1268bc8f45 Adding list_url to r-hms package (#6473) 2017-11-27 14:40:02 -07:00
Michael F. Herbst
3d4e51fad2 Add two test examples to bohrium (#6459) 2017-11-27 13:55:29 -07:00
Eric
dbb329637b r-rtsne: Create new package (#6470) 
* r-rtsne: Create new package

* r-rtsne: add rcpp dependency
 2017-11-27 13:54:53 -07:00
Eric
ebd796110d r-pcapp: Create new package (#6468) 2017-11-27 13:54:36 -07:00
Satish Balay
23bedc276c plasma: extract plasma changes from xsdk-0.3.0 (#6280) 
* plasma: extract plasma changes from xsdk-0.3.0

* plasma: cleanup per review
- netlib-lapack: add support for spec['lapack:c'].libs, spec['blas:c'].libs
- add getblaslapacklibs() to eliminate duplicate code in edit() and build_targets()
- eliminate string manipulation of ld_flags

- remove gfortran check (will check later)
- remove build() (will check later)

* netlib-lapack: fix tuple per review

* netlib-lapack: use  spec[lapack:c,fortran]
 2017-11-27 11:38:10 -08:00
Adam Fidel
557309618f New Package: GAP Benchmark Suite (#6452) 2017-11-27 06:50:49 -07:00
Choong Jun Jin
45e1562162 fixed glog compilation for < 0.3.5 (#6463) 2017-11-27 06:50:26 -07:00
Massimiliano Culpo
eacaa1551e
r-rcpp: adds new versions, fixes failing download in Travis CI (#6464) 2017-11-27 10:15:47 +01:00
Eric
fcf331f176 r-tsne: Create new package (#6461) 2017-11-27 09:30:52 +01:00
Eric
0bb789eb23 r-rcpp: fix list_url to install archived versions (#6462) 2017-11-27 09:20:49 +01:00
peetsv
09eeb991a2 dialign-tx adding patch for gcc@5.4.0 (#6413) 2017-11-26 16:14:18 -07:00
Michael F. Herbst
41eb496021 New Package: Add libcint to spack (#6456) 
* Add libcint to spack

* Clearifying comment
 2017-11-25 21:01:30 -07:00
Michael F. Herbst
178381edf9 Implement opencv libs property (#6457) 2017-11-25 21:00:18 -07:00
Eric
9b5e3434ad r-sn: Create new package (#6433) 
* r-sn: Create new package

* r-sn: fix whitespace and depends_on
 2017-11-25 12:50:13 -07:00
Axel Huebl
a465bf3bec pocl: fix link to libtool (#6440) 
libtool is also needed for linking, otherwise downstream
dependencies such as clfft will fail linking against pocl's
libOpenCL.so with errors such as:

```
  >> 182   /usr/bin/ld: warning: libltdl.so.7, needed by /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so, not found (try using -rpath or -rpath-link)
  >> 183   /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlinit'
  >> 184   /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlerror'
  >> 185   /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlopen'
  >> 186   /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlsym'
  >> 187   collect2: error: ld returned 1 exit status
```
 2017-11-25 11:55:08 -07:00
Gregory Lee
1f2867415a added intel 18.0.1 compilers (#6381) 2017-11-25 11:49:02 -07:00
Michael F. Herbst
25d7ef495c Expand bohrium package (#6438) 
* GCC greater 4.7 required

* Add variant with opencv extmethods

* Fix and export the config path
 2017-11-25 11:46:32 -07:00
healther
d7344d2987 add package py-linecache2 (#6448) 2017-11-25 11:42:16 -07:00
healther
8c5c46a7a2 add missing dependencies to py-pylint (#6445) 2017-11-25 11:41:45 -07:00
healther
835b1ff03d add missing build dependency to py-execnet (#6443) 2017-11-25 11:40:53 -07:00
Axel Huebl
ed685b0262 gearshifft: enable OpenCL (#6441) 
With pocl builds fixed, we can now also use the OpenCL
implementations in gearshifft :)
 2017-11-25 11:40:12 -07:00
healther
86e771bdb3 add missing dependency to py-scikit-image (#6446) 2017-11-25 11:39:16 -07:00
healther
ca90372f74 add missing dependency to py-unittest2 (#6447) 2017-11-25 11:38:42 -07:00
healther
65fd350eb4 add package py-setuptools-scm (#6449) 2017-11-25 11:38:10 -07:00
healther
0c7cf0c7a4 add package py-traceback2 (#6450) 2017-11-25 11:37:38 -07:00
健美猫
0d91f51a27 Python: add 3.6.3 . (#6454) 2017-11-25 11:34:24 -07:00
健美猫
086a1cfe7e r: add version 3.4.2. (#6455) 2017-11-25 11:34:05 -07:00
healther
7c174f11ec add new version to node-js (#6444) 2017-11-25 09:30:06 +01:00
Eric
be095fdb21 r-lars: Create new package (#6453) 2017-11-25 09:24:53 +01:00
Robert Cimrman
77bfda4da6 sfepy: Create new package (#6439) 2017-11-24 12:21:09 +01:00
健美猫
70adbaeeba Octave depends on qt+opengl. (#6437) 2017-11-24 09:40:48 +01:00
Massimiliano Culpo
cde5fdde20
Openblas needs FC, not F77 (#6435) 
fixes #5591
 2017-11-24 07:15:01 +01:00
Michael Kuron
ff4a4fcd9e siesta: add netcdf support (#6431) 2017-11-23 13:39:32 -07:00
George Hartzell
2a2670175d boost@1.54 alse needs the call_once patch (#6434) 2017-11-23 20:17:17 +01:00
Michael Kuhn
5bbbfe9446 Introduce virtual dependency pkgconfig (#5198) 
There are two providers, pkgconf and pkg-config, with the former being
the default provider.
 2017-11-23 08:05:38 -07:00
Sergey Kosukhin
7f0659f032 New version and patch for 'sqlite'. (#6303) 2017-11-23 08:04:41 -07:00
Audrey Thoma
cd7d812be9 express: new package (#6281) 2017-11-23 08:04:02 -07:00
Ondřej Čertík
7a2b3b2588 Add a patch for Intel 18.0.1 (#6392) 2017-11-23 07:28:35 -07:00
Michael F. Herbst
a955f63530 Add bohrium to spack (#6395) 
* Add bohrium package.py

* Changes suggested by @davydden

* Add +cuda guard

* Specify required environment setup
 2017-11-23 07:24:55 -07:00
Eric
1dba6435bd r-plotly: Create new package (#6423) 2017-11-23 07:17:17 -07:00
Denis Davydov
ddf10fa322 dealii: limit CMake to 3.9 as 3.10.0 is not supported yet (#6427) 2017-11-23 07:16:44 -07:00
sknigh
e2cf933ec1 gcc environment module will set CC, CXX, FC, F77, and F90 flags (#3954) 2017-11-23 12:44:55 +01:00
Cameron Smith
951679376e zoltan: add optional dependency on parmetis (#6387) 2017-11-23 09:03:02 +01:00
Eric
6fd1009081 r-mixtools: Create new package (#6421) 2017-11-23 09:01:10 +01:00
Eric
bdd8bb1fd9 r-ranger: Create new package (#6422) 2017-11-23 09:00:32 +01:00
Chien-Chang Feng
630d7e19db py-yt: Yt-project is moved. Add new version. (#6409) 2017-11-23 07:25:35 +01:00
Jon Rood
8b63cc6ad6 Using MPI environment compiler variables for pnetcdf. (#6424) 2017-11-22 21:34:21 -08:00
Massimiliano Culpo
0fc6611dc2
Changed every docs variant into doc as decided in #2663 (#6412) 
fixes #2663
 2017-11-22 15:06:59 +01:00
Sergey Kosukhin
d4ab511f73 Script for 'eccodes' is compatible with Python 3. (#6402) 2017-11-21 15:59:04 -07:00
Audrey Thoma
a0df5ae3e0 phantompeakqualtools: new package (#6403) 2017-11-21 15:58:20 -07:00
Eric
9e013ee036 r-pbapply: Create new package (#6377) 2017-11-21 13:45:12 -07:00
Eric
5a72d30816 r-ggjoy: Create new package (#6399) 2017-11-21 13:44:25 -07:00
Eric
60b50a7bd2 r-ica: Create new package (#6400) 2017-11-21 13:43:02 -07:00
Eric
d6a5310df5 r-cppprogress: Create new package (#6398) 2017-11-21 13:42:44 -07:00
Eric
d725904803 r-sdmtools: Create new package (#6397) 2017-11-21 13:42:28 -07:00
BenBrands
27b9d2614c CMake: add 3.10.0 (#6393) 2017-11-21 08:04:53 -07:00
David Poliakoff
003f83db50 gotcha: new package (#6391) 
* Initial stab at a package for Gotcha

* Commit with no boilerplate

* Flake8
 2017-11-21 08:04:43 -07:00
Audrey Thoma
c4613b8e1f mira: new package (#6385) 2017-11-21 08:04:08 -07:00
Michael F. Herbst
f0c0243cd4 Fix to allow installing pocl 0.14 again (#6372) 
* Resolve issue 4669

* Use prefix path magic attribute
 2017-11-21 08:03:36 -07:00
Yifan Zhu
5250c8eb0a r-broom: new package (#6282) 2017-11-21 10:49:09 +01:00
Yifan Zhu
e3abc7bfa4 r-haven: created new package (#6293) 2017-11-21 09:54:43 +01:00
Yifan Zhu
b7189ecf9e r-psych: created new package (#6286) 2017-11-21 09:40:10 +01:00
Yifan Zhu
ef8429c99c r-modelr: created new package (#6289) 2017-11-21 09:26:44 +01:00
Eric
0743c5bde6 r-crosstalk: Create new package (#6383) 2017-11-20 21:52:58 -07:00
Eric
cd5e6a14bb r-fnn: Create new package (#6384) 2017-11-20 21:52:39 -07:00
Audrey Thoma
8b2abfb28b masurca: new package (#6386) 2017-11-20 21:51:35 -07:00
Eric
70ce7e2099 meme: add version 4.12.0 (#6388) 2017-11-20 21:50:46 -07:00
Eric
035cce2b81 py-biopython: add version 1.70 (#6389) 2017-11-20 21:50:25 -07:00
Eric
17e0b81463 r-ggridges: Create new package (#6376) 2017-11-20 14:18:16 -07:00
Eric
30b794254f py-pysam: add version 0.13 (#6382) 2017-11-20 14:08:25 -07:00
BenBrands
93d5a91a56 dealii: fix HDF5 dependency (#6374) 2017-11-20 11:57:53 -07:00
BenBrands
83db25967e Atlas: add 3.11.39 (#6375) 2017-11-20 11:57:34 -07:00
Eric
9040f34aba r-tclust: Create new package (#6380) 2017-11-20 11:57:04 -07:00
Eric
1d69dbe7ae r-diffusionmap: Create new package (#6378) 2017-11-20 11:56:47 -07:00
Eric
012acdc7a2 r-chemometrics: Create new package (#6379) 2017-11-20 11:56:33 -07:00
Denis Davydov
4e878c21cd elpa: add 2017.05.002 and 2017.05.003 (#5306) 
* elpa: add 2017.05.002 and 2017.05.03
* add a variant for optimization flags
 2017-11-20 11:17:22 -07:00
Denis Davydov
34da07db9b dealii: add cuda_arch variant via CudaPackage (#6070) 2017-11-19 12:39:13 -07:00
Adam J. Stewart
acbdf516f7 Add a new package for rlwrap (#6371) 2017-11-19 06:45:25 -07:00
lingnanyuan
cf3df2a321 r-dose: Create new package. (#6355) 2017-11-18 12:54:14 -07:00
Eric
20092adb94 r-vgam: Create new package (#6363) 2017-11-18 06:39:55 -07:00
Eric
618f4dff6d r-bindrcpp: Create new package (#6366) 2017-11-18 06:36:39 -07:00
Eric
1c55a401b1 r-dtw: Create new package (#6365) 2017-11-18 06:35:47 -07:00
Eric
ebfc7bd7aa r-som: Create new package (#6364) 2017-11-18 06:35:21 -07:00
Michael Kuron
e2fea1e1e6 siesta: new package (#6346) 
* siesta: new package

* siesta: use libs instead of ld_flags everywhere
 2017-11-17 19:01:15 -07:00
Stephen Hudson
b2f0306c6f Mpi4py update (#6342) 2017-11-17 19:00:36 -07:00
Javier Cervantes
21da747a5d hepmc: fix hash and urls, add new version 3.0.0 (#6348) 2017-11-17 18:59:52 -07:00
健美猫
8bc024d2d9 Add cluster.2017.5 and cluster.2018.1. (#6349) 2017-11-17 18:59:18 -07:00
lingnanyuan
9647038f27 r-rvcheck: Create new package. (#6351) 2017-11-17 18:59:00 -07:00
lingnanyuan
eda91bebd7 r-gosemsim: Create new package. (#6352) 2017-11-17 18:58:43 -07:00
lingnanyuan
d836d7e7ea r-do-db: Create new package. (#6353) 2017-11-17 18:58:23 -07:00
lingnanyuan
c604638681 r-fgsea: Create new package. (#6354) 2017-11-17 18:58:01 -07:00
lingnanyuan
5c06255b24 r-clusterprofiler: Create new package. (#6356) 2017-11-17 18:57:40 -07:00
sknigh
1f8f593dd6 Added libhio 1.4.0.0 (#6357) 2017-11-17 18:57:17 -07:00
Brian Homerding
17debcb9b2 NuT: Add Installation of lib and demo app (#6341) 2017-11-16 16:30:42 -07:00
Matthias Vogelgesang
a62f8698c3 Add UFO and dependencies (#6337) 
* Add json-glib

* Add ufo-core

* Add ufo-filters
 2017-11-16 09:37:17 -08:00
healther
ef3c909701 add package py-numba (#6323) 
* add package py-numba

* Update package.py

* Update package.py

* Update package.py
 2017-11-16 10:13:20 -07:00
Audrey Thoma
e941f33eaf meraculous: new package (#6292) 
* meraculous: new package

* adding gcc version conflict

* Update package.py

* Update package.py
 2017-11-16 09:40:46 -07:00
lingnanyuan
bb3d5fd313 r-rhdf5: Create new package. (#6330) 2017-11-16 09:40:15 -07:00
lingnanyuan
e732a554ff r-shortread: Create new package. (#6332) 2017-11-16 09:30:18 -07:00
lingnanyuan
cca06422fa r-sva: Create new package. (#6333) 2017-11-16 09:28:59 -07:00
David Hows
d89b09493c Minor package fixes (#6334) 
* Add no-implicit-fallthrough to MsgpackC

* Add 0.2.1 of Neovim

* Lint
 2017-11-16 09:28:40 -07:00
Stephen Hudson
9d1224e5d8 py-petsc4py: Update version to 3.8.0 and add dependencies (#5792) 
* py-petsc4py: Update version to 3.8.0 and add dependencies

- Added explicit dependency on python and numpy

* Kept old version - and corrected minimal python version

* Update to 3.8.1
 2017-11-15 16:49:36 -07:00
baip
697f3ea71d cp2k: add dependency on smm and libxc & new version 5.1 (#6194) 
* cp2k: add libxsmm dependency

* cp2k: add libxc dependency

* cp2k: add smm variant to select from libxsmm or libsmm

* cp2k: add version 5.1
 2017-11-15 16:49:08 -07:00
Christoph Junghans
7da8a02cbf
git grep --files-with-matches github.com/llnl/spack | xargs sed -i '/github.com/s@llnl/spack@spack/spack@' (#6329) 2017-11-15 16:46:39 -07:00
Denis Davydov
cb5fd6035a intel: add 2018.1 (#6322) 2017-11-15 13:13:15 -07:00
Axel Huebl
d1a733bc86 xtensor, xtl, xsimd (#6315) 
Adds the QuantStack libs (C++, header-only) needed for
xtensor.
 2017-11-15 13:12:31 -07:00
Yifan Zhu
cde0570c56 r-janitor: created new package (#6313) 2017-11-15 13:09:24 -07:00
Yifan Zhu
0d9ab84ebb r-dbplyr: created new package (#6311) 2017-11-15 13:09:11 -07:00
Howard Pritchard
af1b93b3db Open MPI: add 2.0.4 release to package file (#6310) 
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
 2017-11-15 13:03:07 -07:00
健美猫
71f12597a7 Update pgi to 17.10 . (#6306) 2017-11-15 13:02:54 -07:00
Sergey Kosukhin
e77b11674f Update for 'magics' and 'libemos'. (#6275) 2017-11-15 13:01:23 -07:00
Benedikt Riedel
2eb7fabe62 Allow openblas to build on a VM (#6258) 
This adds a "virtual_machine" boolean variant which adds build
options that enable building openblas on a VM.
 2017-11-15 10:32:02 -08:00
Eric
9acf207023 picard: add versions and fix url format (#6309) 2017-11-14 16:41:27 -07:00
Michael Kuhn
ec5d366bcd likwid: Fix hash for 4.3.0 (#6307) 
Prefer 4.2.1 for now because 4.3.0's hash changes regularly.
 2017-11-14 16:41:05 -07:00
健美猫
d9a4e7a038 Update miniconda to 4.3.30. (#6233) 2017-11-14 12:11:53 -08:00
Adam J. Stewart
138e9d08c6 Add the latest version of Lmod (#6297) 2017-11-14 10:32:41 -08:00
koebbe
50957bd44f py-h5py: make sure to depend on the hl variant of hdf5 (#6304) 2017-11-14 09:26:58 -07:00
vishalkenchan
0692029273 update trilinos checksums (#6301) 2017-11-14 09:22:34 -07:00
Michael Kuhn
aa27432a1d ncl: Check for ncl binary after installation (#6298) 
ncl's build system will happily continue in case of errors, which might
result in the ncl binary not being built.
 2017-11-14 09:22:04 -07:00
Michael Kuhn
e31b997162 icu4c: Update to 60.1 (#6295) 
Previous versions try to include xlocale.h, which fails on glibc >= 2.26.
 2017-11-14 09:21:35 -07:00
Yifan Zhu
a8f9182ef3 r-forcats: created new package (#6291) 2017-11-14 09:21:21 -07:00
Michael Kuhn
93bca2f3a2 libbson, libmongoc: Update to 1.8.1 (#6290) 2017-11-14 09:21:05 -07:00
Eric
137a9e64ac trimgalore: add version 0.4.5 (#6288) 2017-11-14 09:20:20 -07:00
Yifan Zhu
392e25b7e6 r-mnormt: created new package (#6287) 2017-11-14 09:20:06 -07:00
Yifan Zhu
05eb287ed9 r-bindr: created new package (#6285) 2017-11-14 09:19:49 -07:00
Yifan Zhu
c042644b53 r-glue: created new package (#6283) 2017-11-13 16:25:52 -07:00
Douglas Duckworth
c7d2b4dbd6 relion 2.1 - update variant defaults (#6201) 
Default precision should be double for CPU. Generally users also want
to use GPUs so the +cuda variant is now also enabled by default.
 2017-11-13 12:29:43 -08:00
Christoph Junghans
bde727e187
mpibash: move to autotools (#6253) 2017-11-13 10:48:31 -07:00
Christoph Junghans
02335fa849
ucx: initial commit (#6265) 2017-11-13 10:47:58 -07:00
Eric
306aca812d ont-albacore: add version 2.1.2 (#6278) 2017-11-13 10:47:40 -07:00
Satish Balay
6fd92e4257 petsc: update to version 3.8.2 (#6244) 
Includes pkgconfig fix [for mfem static build failure]
 2017-11-11 07:16:03 -07:00
Brian Homerding
19f8940c01 Nekbone: Installing data files for example runs (#6243) 
* Nekbone: Installing data files for example runs

* Typo Fix
 2017-11-10 19:59:33 -07:00
Sergey Kosukhin
263126bc5d Create symlink for 'swig' binary after installation. (#6240) 2017-11-10 19:50:11 -07:00
Aaron Fisher
af06ea0e74 Fixed mfem mpi build issue. (#6254) 
* Fixed mfem mpi build issue.

* Fixed a non-mpi build issue and switched to the latest official MFEM release.
 2017-11-10 19:49:17 -07:00
Yifan Zhu
e38f31e773 feature/r-reprex: new package (#6257) 2017-11-10 19:47:21 -07:00
Cyrus Harrison
b079e1dbd5 add alpine ascent (#6224) 
* add ascent package and and deps

* proper use of site_packages_dir prop

* flake8

* add maitain, small updates

* flake8

* flake8

* fixs for docstrings for sphinx
 2017-11-10 17:00:47 -08:00
becker33
917d021997 Add version 1.04 (#6259) 2017-11-10 15:52:48 -08:00
becker33
a7b817b494 elfutils: add --no-as-needed flag for library ordering issue (#6256) 
* add --no-as-needed flag for library ordering issue libelf

* fix syntax error.
 2017-11-10 11:42:37 -08:00
Yifan Zhu
f6ed8d856a xclip: created new package (#6248) 2017-11-10 11:13:00 -07:00
Yifan Zhu
a872dc5927 r-clipr: created new package (#6249) 2017-11-10 11:11:45 -07:00
lingnanyuan
acc3817ffc r-purrr: Create new package. (#6241) 2017-11-09 14:51:30 -07:00
lingnanyuan
65a278c927 r-covr: Create new package. (#6239) 2017-11-09 13:19:53 -07:00
lingnanyuan
e43e29209d r-readxl: Create new package. (#6238) 2017-11-09 13:19:43 -07:00
lingnanyuan
0902f58f3d r-cellranger: Create new package. (#6237) 2017-11-09 13:19:25 -07:00
lingnanyuan
5e0e3092f6 r-rematch: Create new package. (#6236) 2017-11-09 13:19:12 -07:00
Satish Balay
2b07379831 petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configur… (#6189) 
* petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configured with zlib

* petsc: fix dependency [of zlib to be on hdf5 - and not on petsc]

* petsc: use the fact that hdf5/package.py has a hard dependency on zlib [so no need to check for this dependency in code]

recommended-by: @davydden

* petsc: change hdf5 dependency to 'hdf5+hl' as petsc configure is looing for -lhdf5_hl

https://github.com/spack/spack/issues/5846
 2017-11-09 11:34:59 -08:00
Satish Balay
8d512ce9ae magma: cuda updates [from xsdk-0.3.0 branch] (#6160) 
- add gcc dependency per cuda versions
- Fix for cuda-9.0  as it does not support sm20

    nvcc fatal   : Unsupported gpu architecture 'compute_20'
 2017-11-09 11:34:40 -08:00
lingnanyuan
ee867db5de r-log4r: Create new package. (#6133) 2017-11-09 10:23:48 -07:00
Simone Bnà
c79a0fbbf2 mesa: fixed url for version (#5818) 2017-11-09 10:16:52 -07:00