Yifan Zhu
56c7832789
r-iranges: changed url to git and added versioned dependency on r ( #5971 )
2017-10-28 12:14:33 -06:00
Audrey Thoma
f340333e6e
r-geomorph and other r fixes ( #5961 )
2017-10-28 12:13:38 -06:00
lingnanyuan
57611397c9
r-e1071: Add list_url. ( #5986 )
2017-10-28 12:12:52 -06:00
Michael Kuhn
b43e2d2546
likwid: Update checksum ( #6007 )
2017-10-28 12:12:21 -06:00
Yifan Zhu
43c1bb5f30
r-organismdbi: new package ( #5997 )
2017-10-28 12:11:44 -06:00
lingnanyuan
3eab6ed4b2
r-aldex2: Create new package. ( #6015 )
2017-10-28 12:10:22 -06:00
Christoph Junghans
167f7d0cdd
legion: add v17.10.0 ( #6019 )
2017-10-28 12:09:39 -06:00
Audrey Thoma
edae3ceae7
fixing abyss ( #5973 )
2017-10-28 17:05:52 +02:00
Sergey Kosukhin
5ebddcd5e3
Bugfix: from_list_url(). ( #5780 )
...
This fixes a bug in from_list_url where it was referring to a method
which no longer exists. This also adds a test for the from_list_url
function.
2017-10-27 17:41:41 -07:00
Christoph Junghans
95c8ecb6f5
libaec: add v1.0.2 and generic url ( #6017 )
2017-10-27 18:22:27 -06:00
Matthias Diener
45bfcfa30a
Byobu: new package ( #5974 )
2017-10-27 10:43:45 -07:00
Christoph Junghans
f9599c1772
ecp-proxy-apps: add more package ( #6003 )
2017-10-27 08:34:52 -06:00
Christoph Junghans
c97bf0486c
SWFFT: initial commit ( #5953 )
...
* SWFFT: initial commit
* swfft: fix build target
* swfft: add v1.0
* Update package.py
2017-10-27 07:20:29 -06:00
Christoph Junghans
13b41cd53c
comd: add v1.1 ( #5994 )
...
* comd: add v1.1
* Update package.py
* remove serial variant, now ~mpi
* Update package.py
2017-10-27 07:20:18 -06:00
lingnanyuan
222fee1cb3
r-graph: Create new package. ( #5958 )
2017-10-27 08:34:33 +02:00
lingnanyuan
f244653496
r-category: Create new package. ( #5959 )
2017-10-27 08:34:16 +02:00
lingnanyuan
715a679245
r-methodss3: Create new package. ( #5960 )
2017-10-27 08:32:20 +02:00
lingnanyuan
737f9eee5c
r-oo: Create new package. ( #5962 )
2017-10-27 08:31:46 +02:00
lingnanyuan
f676d8f3d7
r-utils: Create new package. ( #5964 )
2017-10-27 08:31:26 +02:00
lingnanyuan
3bb4572e81
r-pfam-db: Create new package. ( #5965 )
2017-10-27 08:27:19 +02:00
lingnanyuan
95ece343c4
r-oligoclasses: Create new package. ( #5966 )
2017-10-27 08:26:25 +02:00
Yifan Zhu
3ea6a11043
r-interactivedisplaybase: created new package ( #5967 )
2017-10-27 08:26:02 +02:00
lingnanyuan
c672b2b191
r-annotationforge: Create new package. ( #5968 )
2017-10-27 08:25:12 +02:00
lingnanyuan
57528fddbb
r-gostats: Create new package. ( #5969 )
2017-10-27 08:24:49 +02:00
Audrey Thoma
835e6107fe
r-mcmcglmm: new package ( #5970 )
2017-10-27 08:24:28 +02:00
Yifan Zhu
7b0fd6510c
r-annotationhub: created new package ( #5972 )
2017-10-27 08:23:25 +02:00
Denis Davydov
c2094a11e3
gnuplot: add 5.2.0 and 5.0.7 ( #5979 )
2017-10-27 08:20:34 +02:00
lingnanyuan
dc8a0e8410
r-deseq2: Create new package. ( #5981 )
2017-10-27 08:16:40 +02:00
lingnanyuan
1de2109a5a
r-agdex: Create new package. ( #5983 )
2017-10-27 08:16:04 +02:00
lingnanyuan
82b1731ded
r-agilp: Create new package. ( #5984 )
2017-10-27 08:15:39 +02:00
lingnanyuan
7c56318cb5
r-aims: Create new package. ( #5987 )
2017-10-27 08:14:55 +02:00
George Hartzell
55b79dca8c
Add info for go@1.9.2 ( #5989 )
...
The go team released 1.9.2 which includes fixes for some things
that 1.9.1 broke:
> ... include fixes to the compiler, linker, runtime, documentation, go command, and the crypto/x509, database/sql, log, and net/smtp packages. They include a fix to a bug introduced in Go 1.9.1 and Go 1.8.4 that broke "go get" of non-Git repositories under certain conditions.
2017-10-27 08:13:33 +02:00
Yifan Zhu
3849401d85
r-annotationfilter: created new package ( #5995 )
2017-10-27 08:09:31 +02:00
Yifan Zhu
0c2a691b1b
r-protgenerics: created new package ( #5998 )
2017-10-27 08:08:16 +02:00
Abhinav Bhatele
ad51e818a7
ecp-proxy-apps: add dependencies ( #5999 )
2017-10-26 19:54:40 -06:00
Christoph Junghans
0b3247c23d
miniamr: bump to v1.4.0 ( #5975 )
2017-10-26 19:51:50 -06:00
Ondřej Čertík
0e464f86bb
Exodus: skip the -G "Unix Makefiles" part ( #5906 )
...
* Exodus: skip the -G "Unix Makefiles" part
The problem is that spack passes -G "Unix Makefiles" into cmake, which normally
works. But in the Exodus package, it is being passed into a bash wrapper
script. In there, the $@ then loses the information about "Unix Makefiles"
being just one argument, and in effect passes -G Unix Makefiles into the cmake
(without quotes), and so cmake only sees -G Unix, and then fails. This is a
known problem with bash with no simple solutions. As a workaround, this patch
skips the first two arguments, i.e., -G and "Unix Makefiles". This makes it
work.
Fixes #5895 .
* Port exodusii to cmake
The cmake options were taken from the cmake-exodus bash script and ported to
spack directly.
* Use variant forwarding to forward the 'mpi'
Now instead of
spack install exodusii~mpi^netcdf~mpi^hdf5~mpi
one can just use
spack install exodusii~mpi
2017-10-26 13:50:18 -06:00
Christoph Junghans
5c09176014
minife: version bump to v2.1.0 ( #5985 )
2017-10-26 11:45:40 -06:00
Abhinav Bhatele
0ff1fe90fa
Laghos: new package ( #5956 )
2017-10-26 09:18:57 -06:00
Abhinav Bhatele
02744141e9
sw4lite: fix build errors and add variants ( #5944 )
...
* sw4lite: fix build errors and add variants
* sw4lite: change linking against blas and lapack
* change order of blas and lapack
* satisfy flake8 requirements
* Update package.py
2017-10-26 09:18:05 -06:00
Jon Rood
18d2fe7647
Customization of the Paraview module file to its nonstandard directory structure ( #5799 )
...
* Add the custom paraview lib directory structure to the library paths in the paraview module file.
* Fixing flake8 issues.
* Checking if lib64 exists for paraview module file generation, else use lib.
* Fixing more flake8 problems I introduced.
2017-10-26 11:12:04 +02:00
Christoph Junghans
a05bbd7104
flang: fixed llvm dep ( #5948 )
...
* flang: fixed llvm dep
* add support for llvm-5
* Update package.py
* Update package.py
2017-10-26 09:34:33 +02:00
Johann Klähn
306f536138
Add option to install clang python bindings to llvm ( #5774 )
2017-10-26 01:46:03 +02:00
Ondřej Čertík
89b0a09de0
Make clang use libc++ by default ( #5943 )
...
Since LLVM 3.9 Clang can use the libc++ library by default using the
CLANG_DEFAULT_CXX_STDLIB cmake configuration variable, without having to
specify the -stdlib=libc++ option on the clang++ command line.
This commit makes clang++ use libc++ by default for LLVM 3.9 and later if the
libcxx variant is on.
Fixes #5942 .
2017-10-25 16:19:32 -06:00
mmwolf
ffb4251666
adding miniTri miniapp ( #5935 )
2017-10-25 15:49:22 -06:00
Omar Padron
dd39862a80
boost: remove duplicate patch ( #5934 )
2017-10-25 12:00:50 -07:00
Jimmy Tang
1f4089a78f
tweak opencv version ( #5623 )
2017-10-25 14:37:40 +02:00
Sergey Kosukhin
c9810f8088
Update for 'netcdf'. ( #5819 )
2017-10-25 14:30:58 +02:00
Audrey Thoma
d839012e00
delly2: new package ( #5820 )
2017-10-25 13:55:13 +02:00
David Hows
05b3178ca4
Zlib gets a 50-60% performance win when compiled with -O2 ( #5838 )
...
Chasing a performance regression has lead me to this change, going from default optimization gives a significant performance win. The sweet spot for zlib is apparently `-O2`, both `-Ofast` and `-O3` are slightly worse (regression is about 3% compared with `-O2) in my testing.
Happy to share my methodology with people so we can benchmark on a wider variety of systems.
2017-10-25 13:53:35 +02:00
Sergey Kosukhin
ce8a698b48
Update for 'eccodes'. ( #5899 )
2017-10-25 13:48:55 +02:00
George Hartzell
5d3a774587
Add package for scalpel@0.5.3 ( #5901 )
...
* Add package for scalpel@0.5.3
Scalpel's a bit of a mess, it expects it's users to just unpack the
tarball, build it in the resulting directory and install that
directory onto their PATH. My install step recapitulates this into
prefix.bin. The alternative was rewiring their scripts (perl), which
use `FindBin` and expect things to be located in the same dir that the
script itself is.
Sigh.
Lightly tested on CentOS 7.
* Flake8 cleanup
* Additional flake8 cleanup
2017-10-25 13:48:11 +02:00
Audrey Thoma
729c88f068
adding perl-bio-perl and dependencies ( #5845 )
...
* perl-bio-perl and dependencies
* minor fixes
* condensing code
* fixing doc error
2017-10-25 13:35:17 +02:00
Sergey Kosukhin
b92ddd72dd
Update for 'cdo'. ( #5947 )
2017-10-25 13:24:19 +02:00
Eric
e2ef033855
bwa: add 0.7.17 ( #5902 )
...
* bwa: add 0.7.17
* bwa: add 0.7.13
2017-10-25 12:21:18 +02:00
George Hartzell
ff031de800
Add old version to bcftools ( #5907 )
...
* bcftools v1.2 and htslib v1.2
* dependency change - only require dependencies for v1.2
2017-10-25 12:20:42 +02:00
Audrey Thoma
9947306c3e
py-xlsxwriter: new package ( #5918 )
2017-10-25 12:19:59 +02:00
George Hartzell
4fb46501af
adding bedtools2 v2.23.0 ( #5911 )
2017-10-25 12:16:10 +02:00
George Hartzell
98c06eae92
Parallel fix sbangs ( #5910 )
...
* Added procedure to edit sbangs of the parallel perl scripts.
* Specify the types of perl dependency
Adding ", type=('build', 'run')" to the dependency declaration to clarify when and how perl is required
* flake8 cleanup
2017-10-25 12:15:10 +02:00
Audrey Thoma
3265008ad2
adding perl-moose and dependencies ( #5912 )
...
* adding perl-moose and dependencies
* added missing dependency
* fixed flake8 errors
2017-10-25 12:07:20 +02:00
Robert Pavel
9e1341a162
Added Hypre Dependency to mfem+hypre ( #5929 )
...
Added missing hypre defendency from mfem's hypre-enabled version
2017-10-25 12:03:50 +02:00
lingnanyuan
acbd6c9f62
r-geneplotter: Create new package. ( #5924 )
2017-10-25 12:01:19 +02:00
lingnanyuan
79b49d44af
r-gridextra: Update version to 2.3 ( #5915 )
2017-10-25 11:50:16 +02:00
Audrey Thoma
f8b90d50de
r-geiger and dependencies ( #5933 )
2017-10-25 11:17:37 +02:00
lingnanyuan
cc51cc0b06
r-rbgl: Create new package. ( #5931 )
2017-10-25 11:17:29 +02:00
Yifan Zhu
f87c426a6c
r-variantannotation: created new package ( #5932 )
2017-10-25 11:17:15 +02:00
lingnanyuan
f1c06dec7c
r-gseabase: Create new package. ( #5930 )
2017-10-25 11:17:00 +02:00
Yifan Zhu
054cc5d361
r-bsgenome: created new package ( #5928 )
2017-10-25 11:16:53 +02:00
Yifan Zhu
6b6d5d20e2
r-lsei: new package ( #5926 )
2017-10-25 11:16:46 +02:00
Yifan Zhu
fc3d484784
r-yarn: created new package ( #5925 )
2017-10-25 11:16:41 +02:00
lingnanyuan
d0a5f73a94
r-formula: Update version to 1.2-2 ( #5923 )
2017-10-25 11:16:34 +02:00
Yifan Zhu
c5447d7818
r-quantro: created new package ( #5922 )
2017-10-25 11:16:20 +02:00
lingnanyuan
05997460f6
r-scales: Update url. ( #5921 )
2017-10-25 11:16:00 +02:00
Yifan Zhu
3216daa905
r-doparallel: added list_url and version 1.0.11 ( #5920 )
2017-10-25 11:15:49 +02:00
lingnanyuan
21799cbe81
r-hmisc: Create new package. ( #5919 )
...
* r-hmisc: Create new package.
* Correct format.
2017-10-25 11:15:40 +02:00
Yifan Zhu
5742ec4fea
r-openssl: changed homepage url to the CRAN package homepage, added list_url and added version 0.9.7 ( #5848 )
2017-10-25 11:12:31 +02:00
Praveen C
5b9de2eaba
Glibc 2.26 does not provide xlocale.h ( #5862 )
2017-10-25 10:39:32 +02:00
Ondřej Čertík
882480fad6
gdbm: pass in proper CPPFLAGS ( #5893 )
...
The problem was that the configure script was not using spack's compiler
wrappers. We now pass the proper compiler wrapper using the CC argument
explicitly.
Fixes #5892 .
2017-10-25 07:09:41 +02:00
Abhinav Bhatele
b47ff33f11
Add a new package for AMG and fix build issues in the amg2013 package ( #5909 )
...
* amg2013: fix build issues
* amg: add new package
* Update package.py
* amg2013: standardize option name
* amg: standardize option names
2017-10-24 21:06:33 -06:00
Ondřej Čertík
39616a2fe1
hypre: make mpi dependency optional ( #5905 )
2017-10-24 18:53:12 -07:00
Robert Pavel
68f7b7863a
Added Spackage for SW4Lite proxy ( #5917 )
...
Added Spackage for C version of SW4Lite proxy. Fortran will follow once
race conditions involving .mod files are resolved
2017-10-24 15:31:05 -06:00
Denis Davydov
31813ef2c7
slepc and petsc version updates ( #5863 )
...
slepc: add 3.8.0
petsc: no longer prefer 3.7.7
2017-10-24 10:57:14 -07:00
Yifan Zhu
8c306b7b83
r-minfi: created new package ( #5887 )
2017-10-24 14:07:45 +02:00
健美猫
37ce53c48f
Add a package: thrust. ( #3729 )
2017-10-24 11:39:38 +02:00
Yifan Zhu
1ee60e7c63
r-nlme: added list_url and version 3.1-131 ( #5890 )
2017-10-24 11:30:49 +02:00
Yifan Zhu
2a2203895a
r-genomicalignments: created new package ( #5785 )
...
* r-genomicalignments: created new package
* r-genomicalignments: using git repo source instead
2017-10-24 11:30:33 +02:00
Yifan Zhu
a68f9dcc26
r-reshape: created new package ( #5889 )
2017-10-24 11:29:56 +02:00
Yifan Zhu
43d39a6b00
r-data-table: added list_url and version 1.10.4-2 ( #5888 )
2017-10-24 11:29:42 +02:00
lingnanyuan
896d4c8d0c
r-mass: Update version to 7.3-47 ( #5885 )
2017-10-24 11:27:04 +02:00
lingnanyuan
cc06112959
r-acepack: Create new package. ( #5884 )
2017-10-24 11:26:37 +02:00
lingnanyuan
b09f0cdbe1
r-latticeextra: Create new package. ( #5883 )
...
* r-latticeextra: Create new package.
* r-latticeextra: Update list_url.
2017-10-24 11:26:20 +02:00
lingnanyuan
01215d705f
r-htmltable: Create new package. ( #5882 )
2017-10-24 11:25:58 +02:00
lingnanyuan
8c0b95c398
r-htmlwidgets: Update verion to 0.9 ( #5881 )
2017-10-24 11:25:42 +02:00
lingnanyuan
22e96a10ad
r-checkmate: Create new package. ( #5880 )
2017-10-24 11:25:24 +02:00
Yifan Zhu
17d94a5b51
r-geoquery: created new package ( #5879 )
...
* r-geoquery: created new package
* r-geoquery: added versioned dependency on r
2017-10-24 11:25:02 +02:00
lingnanyuan
25d38fe077
r-knitr: Update version to 1.17. ( #5878 )
2017-10-24 11:24:45 +02:00
Yifan Zhu
bba655d6d7
r-httr: added list_url and version 1.3.1 ( #5877 )
2017-10-24 11:24:29 +02:00
lingnanyuan
d4d44f0c63
r-rcpparmadillo: Create new package. ( #5875 )
2017-10-24 11:24:16 +02:00
Yifan Zhu
eeb1edd8e5
r-curl: added list_url and version 3.0 ( #5874 )
2017-10-24 11:23:54 +02:00
lingnanyuan
859b9972d3
r-yaml: Update version to 2.1.14 ( #5856 )
2017-10-24 11:23:38 +02:00
