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Author SHA1 Message Date
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
Jon Rood
c0b2e7db73 Add OpenFAST package (wind turbine simulation tool). (#5662) 
* Add OpenFAST package (wind turbine simulator).
* Adding maintainer to openfast package.
* Fixing copyright date.
 2017-10-12 11:42:51 -07:00
Denis Davydov
1b53e82348 various fixes for macOS high sierra (#5647) 
* various fixes for macOS high sierra

* add macOS_version() helper function

* flake8 fixes

* update oce and trilinos

* fix bison
 2017-10-12 11:41:57 -07:00
Carlos Bederián
db149876a4 samtools: add version 1.6 + some fixes (#5715) 
* htslib: add version 1.6

* samtools: add version 1.6, remove zlib dependency

* bcftools: add version 1.6, switch to using standalone htslib
 2017-10-12 10:08:31 -06:00
Audrey Thoma
87c65fafa9 minimap2: new package (#5722) 2017-10-12 10:07:42 -06:00
David Hows
90cd075277 Initial version of libpcap (#5710) 
Add a package script for libpcap with the current version (1.8.1)
 2017-10-12 07:00:21 -06:00
Yifan Zhu
e807397074 r-affy: added versioned dependency on r (#5660) 2017-10-11 19:49:48 -06:00
Yifan Zhu
36eba3bf58 r-affyio: added versioned dependency on r (#5661) 2017-10-11 19:49:28 -06:00
Yifan Zhu
db0fec4d09 r-biocinstaller: added versioned dependency on r (#5663) 2017-10-11 19:49:08 -06:00
Yifan Zhu
4e8ac1d525 r-matrixstats: created new package (#5682) 2017-10-11 19:48:39 -06:00
Yifan Zhu
5e41ad6fed r-biocgenerics: added version 0.22.1 and added versioned dependency on r (#5683) 2017-10-11 19:48:19 -06:00
Yifan Zhu
8d48f07de1 r-genomeinfodbdata: added versioned dependency on r (#5685) 2017-10-11 19:48:00 -06:00