Commit graph

4872 commits

Author SHA1 Message Date
Yifan Zhu
2a7027e2cc r-pcamethods: created new package (#6041) 2017-10-30 22:39:29 -06:00
Yifan Zhu
cbb433655c r-proxy: created new package (#6039) 2017-10-30 22:39:05 -06:00
lingnanyuan
8271434632 r-backports: Create new package. (#6040) 2017-10-30 22:38:35 -06:00
lingnanyuan
81d3c9fdc6 r-biovizbase: Create new package. (#6042) 2017-10-30 22:38:10 -06:00
Abhinav Bhatele
b37c8fef74 ecp-proxy-apps: release number changed to 1.0 (#6049) 2017-10-30 22:37:09 -06:00
Abhinav Bhatele
347c76b7a0 comd: update the git repo (#6027)
git repo has moved from exmatex to ECP-copa
2017-10-30 14:47:16 -06:00
George Hartzell
e6bc45a04a Add bowtie2@2.3.0, fix dependencies and sbangs (#5834)
* Add bowtie2@2.3.0, fix dependencies and sbangs

Add support for bowtie2@2.3.0

- digest
- a patch for 2.3.0 that parallels the existing package.  Truth be
  told it builds (for me) without this, but I'm assuming that they're
  there for a reason...).
- tune up dependencies
  - need tbb
  - don't need readline or zlib

Several things were installed with sbang's that use `/usr/bin/env` to
fine perl or python.  Fix the dependency and clean up the sbang lines.

* Fix python exe name, avoid path banging

I'd cut and pasted the python bit from the perl bit and missed one
reference to perl.

While I'm there, use the cleaner `spec['perl'].command` instead of
banging together the path from its bits.

* Fix up the "when" constraints on the dependencies

Get the edge cases right.

- 2.2.5 doesn't need tbb, 2.3.[01] do.
- 2.3.1 needs readline and zlib.
2017-10-29 15:40:00 -06:00
Denis Davydov
957ded209a add updated 2017 versions of Intel packages (#5957) 2017-10-29 15:38:10 -06:00
mmwolf
73fb02229a Changed from setting C compiler to setting C++ compiler (#6011) 2017-10-29 07:42:27 -06:00
Denis Davydov
f6a8ae230e dealii: remove bzip2 dependency for newer versions (#6022) 2017-10-29 07:39:51 -06:00
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
lingnanyuan
ae578069bd r-formatr: Update version to 1.5 (#5855) 2017-10-24 11:23:17 +02:00
lingnanyuan
050b753bb7 r-crayon: Update version to 1.3.4 (#5854) 2017-10-24 11:23:00 +02:00
lingnanyuan
764b7a7ad1 r-sourcetools: Create new package. (#5853) 2017-10-24 11:22:42 +02:00
lingnanyuan
4b50598252 r-testit: Update version to 0.7 (#5852) 2017-10-24 11:22:23 +02:00
lingnanyuan
6b87875d81 r-markdown: Update version to 0.8. (#5851) 2017-10-24 11:22:05 +02:00
Yifan Zhu
ab96705f05 r-base64: created new package (#5850) 2017-10-24 11:21:48 +02:00
Yifan Zhu
f814e9bba1 r-illuminaio: created new package (#5849) 2017-10-24 11:21:31 +02:00
lingnanyuan
7a176ca89e r-evaluate: Update version to 0.10.1. (#5847)
* r-evaluate: Update version to 0.10.1.

* r-evaluate: update list_url.
2017-10-24 11:20:47 +02:00
lingnanyuan
420048350f bioconductor update (#5786)
* r-a4: Add r dependency and update url.

* r-a4base: Add r dependency and update url.

* r-a4classif: update url and add r dependency.

* r-a4core: Update url and add r dependency.

* r-a4preproc: Update url and add r dependency.

* r-a4reporting: Update url and add r dependency.

* r-abaenrichment: Update url and add r dependency.

* r-absseq: Update url and add r dependency.

* r-acgh: Update url and add r dependency.

* r-acme: Update url and add r dependency.

* r-adsplit: Update url and add r dependency.

* r-affxparser: Update url and add r dependency.

* r-affycomp: Update url and add r dependency.

* r-affycompatible: Update url and add r dependency.

* r-affycontam: Update url and add r dependency.

* r-annaffy: Update url and add r dependency.

* r-annotate: Update url and add r dependency.

* r-annotate: Update url and add r dependency.

* r-annotationdbi: Update url and add r dependency.

* r-genefilter: Update url and add r dependency.

* r-mlinterfaces: Update url and add r dependency.

* r-limma: Update url and add r dependency.

* r-multtest: Update url and add r dependency.

* r-a4classif: Correct format.

* r-affycomp: Correct error.
2017-10-24 11:19:19 +02:00
Yifan Zhu
f9f0c1472f r-siggenes: new package (#5831)
* r-siggenes: created new package

* deleted extra indent
2017-10-24 11:14:04 +02:00
lingnanyuan
cea33af464 r-affyrnadegradation: Create new package. (#5830) 2017-10-24 11:13:53 +02:00
lingnanyuan
2ede483149 r-affyqcreport: Create new package. (#5829) 2017-10-24 11:13:44 +02:00
Yifan Zhu
edac742f84 r-nor1mix: created new package (#5828) 2017-10-24 11:13:04 +02:00
lingnanyuan
46b385761d r-affyplm: Create new package. (#5827) 2017-10-24 11:12:56 +02:00
lingnanyuan
2c5b3a2268 r-affypdnn: Create new package. (#5826) 2017-10-24 11:12:47 +02:00
Yifan Zhu
6fd0030acb r-beanplot: created new package (#5825)
* r-beanplot: created new package

* correct according to flake8
2017-10-24 11:12:15 +02:00
Aaron Fisher
204217f7c1 Updated external package versions. (#5833) 2017-10-24 11:10:59 +02:00
Yifan Zhu
968144f1c5 r-bumphunter: new package (#5824)
* r-bumphunter: created new package

* r-bumphunter: added description
2017-10-24 11:09:38 +02:00
Sergey Kosukhin
161dca6d5d Update for 'hdf5'. (#5790)
* Refactoring for 'hdf5'.

* Remove 'unsupported' variant.
2017-10-24 11:09:08 +02:00
Michael Kuhn
c7ac4e3774 go: Update to 1.9.1 (#5868) 2017-10-24 11:02:33 +02:00
Todd Gamblin
5449884b2e Fix bare 'except:' to placate errors in new flake8 version.
- fixes E722 errors from latest version of flake8
- requires us to not use 'bare except:' and catch BaseException instead
2017-10-24 10:05:36 +02:00
Todd Gamblin
0bb1eb32f2 fix bugs found with stricter flake8 rules
- When you don't use wildcards, flake8 will find places where you used an
  undefined name.

- This commit has all the bugfixes resulting from this static check.
2017-10-24 10:05:36 +02:00
Todd Gamblin
7dd79094b0 remove wildcards from make spack core and packages
- This removes all wildcard imports EXCEPT `from spack import *` in packages
2017-10-24 10:05:36 +02:00
Todd Gamblin
beab0cb92e add newlines at end of some package files 2017-10-24 10:05:36 +02:00
Mark Grondona
328dc3d140 jansson: enable shared library (#5857)
Jansson builds only a static library by default, which is probably
not what most users want. Add Cmake args required to build a shared
library and enable those via a default 'shared' variant of the
package.
2017-10-23 13:32:51 +02:00
jiseung
969c8b177f new package: hpgmg (#4888)
* new package: hpgmg

* removed build and changed extend() to append()

* changes based on comments

* pep8 compliant

* addressed rest of comments

* trigger checks

* changed from fe_fv to two boolean variants

* fixed compilation issues

* cleared up ambiguities in solver variants

* removed +mpi condition

* changes based on review
2017-10-20 17:34:55 -07:00
George Hartzell
c9d9901e43 perl: add old version (#5844) 2017-10-20 16:18:24 -07:00
Christoph Junghans
2e1a96f262 xsbench: add v14 (#5835) 2017-10-20 08:52:17 +02:00
Milton Woods
d72bcc91f4 perl: ignore perllocal.pod files during package activation (#5271) 2017-10-19 14:24:49 -07:00
George Hartzell
b46f1e3605 bcl2fastq needs with working_dir: after changes in #5776 (#5803)
#5776  cleaned up the way the the current working directory is
managed (less magic state).

bcl2fastq is packaged like a russian doll, rather than an archive file
that contains the source, there's a zip file that contains a tar.gz
file that contains the source.  The package definition has a bit of
extra code that unpacks the inner tarball.

That extra bit of code now needs to explicitly arrange to be in the
correct directory before it does its work.
2017-10-19 08:59:25 +02:00
Christoph Junghans
4774c9887e libxml2: use spack's xz (#5816) 2017-10-19 08:32:37 +02:00
lingnanyuan
6642f62eb9 r-affyexpress: Create new package. (#5807) 2017-10-18 19:07:04 -06:00
Yifan Zhu
5e2c4dbb5c r-rtracklayer: new package (#5808) 2017-10-18 19:06:36 -06:00
lingnanyuan
76cce82d65 r-affyilm: Create new package. (#5810) 2017-10-18 19:06:16 -06:00
Yifan Zhu
d701c4afd6 r-genomicfeatures: new package (#5811)
* r-genomicfeatures: created new package

* modified version number and added versioned dependency on r

* fixed typo
2017-10-18 19:05:53 -06:00
Denis Davydov
3e67b98e29 dealii: blacklist boost 1.64 and 1.65 (#5805)
* dealii: blacklist boost 1.64 and 1.65

* flake8
2017-10-18 15:58:05 -06:00
Stephen Hudson
0b62625e9d py-mpi4py: Add develop version and dependencies (#5798)
* py-mpi4py: Add develop version and dependencies

- Add cython dependency for develop version

- Add explicit python dependency

* py-mpi4py: Specify 2.0.1 instead of develop for conditional dep
2017-10-18 15:56:48 -06:00
Akhil Reddy Patlolla
9b994c05f4 CoMD Proxy App with Serial, MPI, OpenMP Support (#4864) 2017-10-17 19:59:57 -06:00
George Hartzell
ad5fb40d75 perl: add write permissions to update config files (#5746)
Perl installs a couple of config files that need to be munged so that
they don't refer to the spack compiler.  These files are installed
read-only.  Behind the scenes 'filter_file' moves its file to a safe
place, and tries to create a working file that is both O_WRONLY and
has the perms of the original file.  On an NFSv4 filesystem, the
combination of 'r--r--r--' and O_WRONLY throws a permissions error.

This commit adds a simple context manager that temporarily makes the
files writable.
2017-10-17 18:38:23 -07:00
David Hows
ffc4c31b82 Add a new +clanglibcpp option for Boost (#5708)
* Add a new +clanglibcpp option for Boost

Currently, the compile of boost with clang will use the stdlibc++. This patch adds an optional flag to use clangs included libc++ instead.

* Linting

Fix long lines and white space errors
2017-10-17 01:40:09 -07:00
Christoph Junghans
5f592fb911 votca-xtp: added url (#5772) 2017-10-17 01:39:02 -07:00
Christoph Junghans
244c7af864 flang: clean up (#5766) 2017-10-17 01:38:41 -07:00
Christoph Junghans
1a12e6022b liquo: added 1.3 and develop (#5781) 2017-10-17 01:36:54 -07:00
Douglas Duckworth
f0da8251b3 singularity 2.4 added (#5782) 2017-10-17 01:28:19 -07:00
Todd Gamblin
d14816cbaf Spack tests no longer clutter var/spack/stage
- Tests use a session-scoped mock stage directory so as not to interfere
  with the real install.

- Every test is forced to clean up after itself with an additional check.
  We now automatically assert that no new files have been added to
  `spack.stage_path` during each test.

  - This means that tests that fail installs now need to clean up their
    stages, but in all other cases the check is useful.
2017-10-17 01:26:31 -07:00
Jon Rood
890c5ad329 Forcing Paraview to avoid using git describe to determine its own version number (#5783)
* Forcing Paraview to avoid using git describe to determine its own version number.

* Shortening references to spec in paraview.
2017-10-16 15:32:23 -06:00
Aaron Fisher
639d9c305a Updated the rc tag and version. (#5761) 2017-10-16 11:26:26 -07:00
Christoph Junghans
89344ebd44 portage: fixes + added v1.1.* (#5706) 2017-10-16 09:59:41 -07:00
Michael F. Herbst
d0cf3db46e armadillo: use libs to provide arpack and superlu libraries (#5777) 2017-10-16 12:57:01 +02:00
Denis Davydov
f6c16de6de petsc: a temporary workaround for concretizer bug in all packages which depend on SLEPc (#5755) 2017-10-16 00:53:55 -07:00
Johann Klähn
6c67de48e8 Update llvm to version 5.0.0 (#5773) 2017-10-15 13:04:40 -06:00
Michael F. Herbst
5656554922 Add krims and lazyten (#5771)
* Add krims to spack

* Add lazyten to spack

* Add description for lazyten

* Changes suggested by @davydden and @junghans
2017-10-15 11:45:11 -06:00
Denis Davydov
a16ec21fbe boost: remove preferred 1.63 (#5770)
1.64 had issues serialization (make_array and others) when built with
+mpi+python. It appears that those issues are fixed in 1.65.1
so we can remove preferred tag from 1.63.
2017-10-14 16:50:28 -06:00
Denis Davydov
cfd823c3f7 intel-tbb: add 2018.1 (#5769) 2017-10-14 16:40:23 -06:00
Denis Davydov
dcb888d477 gsl: add 2.4 (#5768) 2017-10-14 16:39:43 -06:00
Denis Davydov
8f52295dd8 oce: add 0.18.2 (#5767) 2017-10-14 16:39:21 -06:00
Christoph Junghans
31115af128 boost: call_once_variadic.patch is already part of 1.56.0 (#5341) 2017-10-14 12:53:25 -06:00
Christoph Junghans
a685372636 Revert "Use cflags instead of the args variable (#5756)" (#5765)
This reverts commit 6c3184820a.
2017-10-14 13:55:02 +02:00
Satish Balay
0168025c1c superlu_dist: update to latest version 5.2.1 (#5762)
The interface to +int64 changed from  -D_LONGINT to XSDK_INDEX_SIZE=64. This change
uses the appropriate interface for for the given version
2017-10-13 21:22:44 -06:00
David Gardner
f885c89fdc Update Sundials package (#5696)
* initial update of sundials package

* fix bugs in initial sundials update

* add xsdk cmake setup, fix generic math option, add cuda/raja Makefiles to install fixes

* Fix lapack install bug, add new conflicts, clean up formatting

* Address pull requeset comments and make fomatting style consistent

Remove blas variant as blas is only needed when used by an external
linear solver. Set related CMake blas variables as needed depending
enabled external linear solvers.

Add minimum required CMake version.

Additional conflicts and dependencies for external libraries based
on mpi, indextype, and precision.

Fix SuperLU_MT logic to check which threading type SuperLU_MT was
configured with.

Add maintaiers.

Change Sundials solver options to use an array of values.

Consistently use % for formatting.

* change triple-single quotes to single quotes

* Change indextype option to a single int64 option
2017-10-13 21:13:10 -06:00
Yifan Zhu
4d3424a5d4 r-preprocesscore: added versioned dependency on r (#5671) 2017-10-13 18:50:26 -06:00
Yifan Zhu
e6109381fc r-rmpi: added list_url and updated md5 (#5698) 2017-10-13 18:35:06 -06:00
Yifan Zhu
ad8b9522d6 r-edger: added versioned dependency on r (#5669) 2017-10-13 18:32:43 -06:00
Yifan Zhu
8c2fe52f8e r-s4vectors: added versioned dependency on r (#5672) 2017-10-13 18:32:17 -06:00
Denis Davydov
c13e13a52b likwid: update versions (#5757) 2017-10-13 16:08:49 -06:00
Yifan Zhu
2c73c9fb50 r-xvector: added versioned dependency on r (#5731) 2017-10-13 16:01:18 -06:00
Satish Balay
6fcfc3bd5a flake8: fix warnings (#5759) 2017-10-13 15:16:58 -06:00
Ondřej Čertík
6c3184820a Use cflags instead of the args variable (#5756)
That way the user can still append things to CFLAGS.
2017-10-13 15:15:06 -06:00
Christoph Junghans
3c7dd367f8 py-espresso: initial commit (#5724) 2017-10-13 12:29:30 -07:00
Christoph Junghans
23e801923d espressopp -> py-espressopp (#5732)
* espressopp -> py-espressopp

* Update package.py
2017-10-13 12:28:36 -07:00
Ondřej Čertík
e76cfbbfd8 Fix m4 to compile with Intel (#5728)
Fixes #5705.
2017-10-13 11:20:49 -06:00
Yifan Zhu
8ffe18f1dc r-biostrings: added versioned dependency on r (#5667) 2017-10-13 07:51:30 -06:00
Yifan Zhu
ce1e5e3098 r-zlibbioc: added versioned dependency on r (#5674) 2017-10-13 07:50:10 -06:00
Denis Davydov
b8c1ce43fa trilinos / oce : add missing if before calling macOS_version (#5743)
* trilinos: add missing if before calling macOS_version

* oce: add missing if before calling macOS_version
2017-10-13 07:49:18 -06:00
Yifan Zhu
9716a6f37f r-readr: created new package (#5741) 2017-10-13 07:47:43 -06:00
Yifan Zhu
350624a231 r-dorng: created new package (#5740) 2017-10-13 07:47:01 -06:00
Yifan Zhu
9f3e055e8b r-stringr: added list_url and version 1.2.0 (#5738) 2017-10-13 07:46:29 -06:00
Yifan Zhu
525b69bbad r-stringi: added list_url and version 1.1.5 and 1.1.3 (#5737) 2017-10-13 07:45:26 -06:00
Yifan Zhu
0b117a03c6 r-summarizedexperiment: created new package (#5734) 2017-10-13 07:45:05 -06:00
Yifan Zhu
501ebe6706 r-yaqcaffy: added list_url and versioned dependency on r (#5730) 2017-10-13 07:44:26 -06:00
Denis Davydov
65f12c8160 slepc: refine version constraints for petsc 3.8 (#5752) 2017-10-13 07:11:17 -06:00
Denis Davydov
22ef8efce9 openblas: remove extra develop version (#5750) 2017-10-13 12:10:05 +02:00
Denis Davydov
b182e2334d gettext: fix prefix (#5749) 2017-10-13 10:52:55 +02:00
Brian Van Essen
bd185b8146 Lbann flags (#5747)
* Fixed the datatype flag in the LBANN package.  Also added develop
version to OpenBLAS.

* Fixed where the datatype flag should be set.
2017-10-12 20:23:38 -06:00
Yifan Zhu
f2a6685d8c r-gcrma: added versioned dependency on r (#5670) 2017-10-12 16:18:30 -06:00
Yifan Zhu
d4906169e0 r-simpleaffy: added versioned dependency on r (#5673) 2017-10-12 16:18:15 -06:00
Satish Balay
59163f9750 petsc: add in maintainers (#5729) 2017-10-12 15:09:47 -06:00
David Hows
8ff8b7476c Add the option for a versioned layout to boost (#5709) 2017-10-12 12:51:39 -06:00
Audrey Thoma
36ed96e7dd kaks-calculator: new package (#5725)
* kaks-calculator: new package

* kaks-calculator: new package

* fixing homepage
2017-10-12 12:47:11 -06:00
Satish Balay
98c2184bd3 petsc: update to latest 3.8 version [and include 3.7.7] (#5723)
Also fix flake8 warning "import os should be before import sys"
2017-10-12 12:46:00 -06:00