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
