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5541 commits

Author SHA1 Message Date
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
Benedikt Riedel
266de67c24 ROOT needs to have a consistent version of binutils, as it is very sensitive to the version of libopcodes. You can't move the code from one system (with the same OS) as another. (#6226) 2017-11-09 06:49:27 -08:00
lingnanyuan
935a6b00d7 r-analysispageserver: Create new package. (#6135) 2017-11-09 07:23:10 -07:00
Levi Baber
74d38b3150 py-dlcpar (#6229) 
* py-dlcpar: new package

* py-dlcpar: whitespace
 2017-11-09 07:21:56 -07:00
baip
acf6653933 pexsi: add version 0.10.2 (#6232) 2017-11-09 07:21:39 -07:00
David Gardner
d9fc26b2a5 add sundials 3.1.0 (#6230) 2017-11-09 14:04:03 +01:00
Luigi Calori
24bb3c61de fix perl dependent modules, #5900 (#5937) 
*  FIX perl dependent environmwent setup to avoid void lines in generated modules as #5900

* remove debug prints

* fix flake8
 2017-11-08 22:10:50 -07:00
Alfredo Adolfo Gimenez
a754bd7eee Package/sosflow (#6122) 
* Added missing deps to libffs

* SOSflow spack package pointing to sos_flow feature/spack branch

* Using tag for spack build

* Change url to spack/spack
 2017-11-08 22:07:37 -07:00
David Gardner
a656bc300a add patch for building sundials (#6161) 
* add patch for building sundials on mac

* add upper limit on the patch
 2017-11-08 22:06:34 -07:00
Yifan Zhu
3159841e33 r-callr: created new package (#6223) 2017-11-08 21:59:21 -07:00
lingnanyuan
72bec9a7a0 r-rex: Create new package. (#6221) 2017-11-08 21:57:09 -07:00
Yifan Zhu
ca2ffd9299 r-rvest: created new package (#6220) 2017-11-08 21:56:50 -07:00
Levi Baber
ef126523f1 fastme: new package (#6219) 2017-11-08 21:56:32 -07:00
Yifan Zhu
edc1e6a0d8 r-selectr: created new package (#6218) 2017-11-08 21:56:02 -07:00
lingnanyuan
e57564e899 r-tseries: Create new package. (#6216) 2017-11-08 21:55:45 -07:00
sknigh
699748a2be Added missing build dependency to json-c (#6211) 2017-11-08 21:55:28 -07:00
lingnanyuan
e2004076b1 r-allelicimbalance: Create new package. (#6044) 2017-11-08 21:52:46 -07:00
Yifan Zhu
ac7f5a1af1 r-mzr: created new package (#6206) 2017-11-08 19:53:00 -07:00
Yifan Zhu
cd4b19ffa8 r-msnbase: new package (#6207) 2017-11-08 19:52:38 -07:00
lingnanyuan
912d39908d r-sqldf: Create new package. (#6208) 2017-11-08 19:52:08 -07:00
lingnanyuan
4585d6426a r-gsubfn: Create new package. (#6209) 2017-11-08 19:51:51 -07:00
Yifan Zhu
b110cd0b12 r-vsn: new package (#6210) 
* r-hexbin: updated md5

* r-vsn: created new package
 2017-11-08 19:51:35 -07:00
lingnanyuan
7848e0d4b6 r-quantmod: Update version to 0.4-11 (#6212) 2017-11-08 19:51:13 -07:00
Yifan Zhu
ecdaea1c8e r-xml2: created new package (#6217) 2017-11-08 19:50:53 -07:00
lingnanyuan
1c2292dcd4 r-timedate: Create new package. (#6215) 2017-11-08 19:50:37 -07:00
lingnanyuan
5558cce438 r-fracdiff: Create new package. (#6214) 2017-11-08 19:50:18 -07:00
lingnanyuan
2cd57876c7 r-forecast: Create new package. (#6213) 2017-11-08 19:49:58 -07:00
Christoph Junghans
b3f678c1c0
gasnet: add 1.30.0 (#6167) 
* gasnet: add 1.30.0

* gasnet: expose more options as variants

* gasnet: change defaults
 2017-11-08 19:43:13 -07:00
Audrey Thoma
877bee3cb5 guidance: new package (#6079) 
* guidance: new package

* not really fixed yet

* adding loop

* fixing url

* dang typos
 2017-11-08 14:07:13 -07:00
lingnanyuan
dd3a6d7f18 r-ampliqueso: Create new package. (#6132) 2017-11-08 14:05:53 -07:00
Yifan Zhu
96f70606e8 r-tiff: created new package (#6134) 2017-11-08 14:05:33 -07:00
lingnanyuan
f73b409968 r-anaquin: Create new package. (#6138) 2017-11-08 14:05:17 -07:00
lingnanyuan
2cba0d4d5f r-qvalue: Create new package. (#6137) 2017-11-08 14:05:00 -07:00
baip
4273ebac3c libxsmm: add libs property (#6193) 2017-11-08 14:04:26 -07:00
lingnanyuan
17b9a479b6 r-aneufinderdata: Create new package. (#6192) 2017-11-08 14:03:35 -07:00
lingnanyuan
bb619aa091 r-aneufinder: Create new package. (#6191) 2017-11-08 14:03:22 -07:00
Christoph Junghans
d8db861fec
flecsi: fix build (#6168) 2017-11-08 14:03:05 -07:00
lingnanyuan
04f32377b2 r-rhtslib: Create new package. (#6164) 2017-11-08 14:02:12 -07:00
Audrey Thoma
3fcc911737 kraken: new package (#6163) 2017-11-08 14:01:55 -07:00
Audrey Thoma
743a87abb3 fpc: new package (#6162) 2017-11-08 14:01:31 -07:00
lingnanyuan
6556a5c914 r-cowplot: Create new package. (#6190) 2017-11-08 13:58:57 -07:00
Yifan Zhu
5f70d578ec r-maldiquant: created new package (#6188) 2017-11-08 13:58:43 -07:00
lingnanyuan
860834e094 r-reordercluster: Create new package. (#6187) 2017-11-08 13:58:21 -07:00
Yifan Zhu
605c8e65b3 r-mzid: created new package (#6186) 2017-11-08 13:58:04 -07:00
Yifan Zhu
98baf49ba6 r-xde: created new package (#6185) 2017-11-08 13:57:46 -07:00
lingnanyuan
3943bc945b r-ggdendro: Create new package. (#6184) 2017-11-08 13:57:30 -07:00
lingnanyuan
241e1b56b5 r-dnacopy: Create new package. (#6183) 2017-11-08 13:57:15 -07:00
Yifan Zhu
92a582d5f8 r-mergemaid: created new package (#6182) 2017-11-08 13:56:59 -07:00
lingnanyuan
146db9adef r-bamsignals: Create new package. (#6181) 2017-11-08 13:56:34 -07:00
Yifan Zhu
87aafeb78a r-xmapbridge: created new package (#6180) 2017-11-08 13:56:15 -07:00
Sergey Kosukhin
c7a855ba57 Missing dependency for 'cdo'. (#6175) 2017-11-08 13:55:57 -07:00
baip
ed00757265 gcc: add 5.5.0 (#6171) 2017-11-08 20:27:08 +01:00
vishalkenchan
392929ba77 lammps: add more packages (#6174) 
* lammps : adding new varients and dependencies therein

* Update package.py

* removing trailing whitespaces
 2017-11-08 09:01:14 -07:00
Matthew Scott Krafczyk
00d48e60bf Fix for nghttp2 installation (#5904) 
nghttp2 depends on python, and requires the install directory to exist,
and contain the python module directory which it will eventually
install the python modules into.
 2017-11-07 15:59:15 -08:00
James Dickson
841d42b308 TyphonIO: new package + Updated MACSio package (#6177) 2017-11-07 13:13:06 -07:00
Audrey Thoma
8bae192d5c repeatmasker: new package (#6108) 2017-11-06 17:27:42 -07:00
Michael Kuhn
ca73103dac Introduce static_to_shared_library function (#6092) 
The static_to_shared_library function takes an existing static library
and produces a shared library based on it.
 2017-11-06 17:21:46 -07:00
Satish Balay
dc78e60c83 trilinos: update hdf5 dependency to use 'hdf5+hl' (#6025) 
* 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

* fix flake8 warning
 2017-11-06 13:03:06 -08:00
Luigi Calori
f0d33df3a9 some missing X11 "*proto" dependencies (#6158) 
* fix xinput deps

* adding other x11 proto missing deps, see #6157
 2017-11-06 13:02:05 -08:00
Satish Balay
436ebc4490 petsc: update petsc dependency on superlu-dist (#6159) 2017-11-06 12:52:10 -08:00
Yifan Zhu
cd4d26705e Bioconductor package url change (#5797) 2017-11-06 11:17:59 -07:00
Michael Kuhn
450f2fa034 likwid: Use external lua if possible (#6009) 2017-11-06 11:14:34 -07:00
Douglas Duckworth
47b15feec3 added new package - MotionCor2 (#6151) 2017-11-06 11:09:46 -07:00
Denis Davydov
f538b7ac3e dealii: make sure bundled libs are not used (#6106) 2017-11-06 12:38:59 +01:00
Besnard Jean-Baptiste
84c6fea32e Graphviz : Add a GTS variant (#6149) 
Enable support for the GNU Triangulated Surface Library

	- New variant +gts for graphviz
	- Optionnal dependency for GTS (already packaged)
 2017-11-05 16:55:44 -08:00
Douglas Duckworth
ccc51cea7d added relion v 2.1 (#6023) 
* added relion v 2.1

* relion 2.1 - misssed comma

* relion now pulling from master branch - removed 2.03 - added cuda 8 as dependency given 9 does not yet work with relion per https://github.com/3dem/relion/issues/296
 2017-11-05 15:01:21 -08:00
Ben Boeckel
22df09315f Re-add list_url for all R packages (#6110) 
* r-igraph: find old packages in the archive

Fixes #6104.

* r-irlba: find old packages in the archive

Fixes #6101.

* r-lazyeval: find old packages in the archive

Fixes #6102.

* packages: set list_url for all packages hosted on CRAN

* packages: consistently use the CRAN archive URLs
 2017-11-05 13:42:24 -08:00
Adam Moody
2a8c97d440 dtcmp: add v1.1.0 (#6146) 2017-11-05 09:25:03 -08:00
Satish Balay
d34d0d6cbc petsc: update to version 3.8.1 (#6150) 
* petsc: update to version 3.8.1

* petsc: add in conflict between petsc-3.8.0 & mkl
 2017-11-05 09:24:42 -08:00
Axel Huebl
5d9dd24daa ISAAC 1.3.3 (#6152) 
Add a new release of ISAAC.
 2017-11-05 09:24:18 -08:00
Todd Gamblin
05fa302655
Replace github.com/llnl/spack with github.com/spack/spack (#6142) 
We moved to a new GitHub org! Now make the code and docs reflect that.
 2017-11-04 17:08:04 -07:00
vishalkenchan
386e0af089 add rol variant (#6105) 2017-11-04 12:14:46 -07:00
Yifan Zhu
9d234c4f8e r-yapsa: created new package (#6121) 2017-11-03 14:21:00 -06:00
Yifan Zhu
fb1160d052 r-keggrest: created new package (#6120) 2017-11-03 14:20:36 -06:00
lingnanyuan
3921948b03 r-statmod: Create new package. (#6119) 2017-11-03 14:20:14 -06:00
lingnanyuan
b204c7e793 r-deseq: Create new package. (#6118) 2017-11-03 14:19:38 -06:00
lingnanyuan
f91c25ddee r-samr: Create new package. (#6117) 2017-11-03 14:19:16 -06:00