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Author SHA1 Message Date
Axel Huebl
427993b951 c-blosc: 1.15.0 (#10009) 
Add latest version of c-blosc.
 2018-12-04 09:10:08 -06:00
Kelly (KT) Thompson
4d26faac81 Provide a new spackage for py-pint. (#9991) 
* Provide a new spackage for py-pint.

Pint is a Python package to define, operate and manipulate physical quantities:
the product of a numerical value and a unit of measurement. It allows arithmetic
operations between them and conversions from and to different
units. https://pint.readthedocs.io/en/latest/

* Switch hash from md5 to sha256.
 2018-12-04 08:58:11 -06:00
Greg Sjaardema
b471e2768b MATIO: New versions (#9993) 
Add several new versions so that current functionality can be accessed.  Current version is now 1.5.13.

Update `url`, `list_url`, and `list_depth` so spack can find available versions
 2018-12-04 08:53:15 -06:00
Oliver Breitwieser
3cf998a5db Add tmux@2.8 (#10010) 2018-12-04 08:37:09 -06:00
Greg Sjaardema
231888f3e9 PNETCDF: Update with current versions (#9982) 
* PNETCDF: Update with current versions

Added latest versions. (1.10.0, 1.9.0, 1.8.1)

* PNETCDF: Revert version change in url

Reverted the change in the url variable version since not required.
 2018-12-04 08:31:41 -06:00
Greg Sjaardema
6e3b016aa2 NETCDF: Add new versions and update url (#9970) 
* NETCDF: Add new versions and update url

Added the 4.6.2 version which was recently released.
Changed the url to point to the official Unidata site and added option to retrieve master version from git.

* NETCDF: checksum and version updates

Reverted back to use of previous URL.  The `https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz` location is newer, but spack does not seem to be able to access all of the versions at that location -- only goes back to 4.5.0.  Since several installations are still providing 4.4.0, thought it best to go back to previous url.  However, it looks like the naming convention has changed since 4.6.2, so need to provide explicit url for 4.6.2.  Probably best to go to a `url_for_version()` scheme if that naming convention stays in place?
 2018-12-04 15:03:25 +01:00
Bert Wesarg
262b3f859e boost: 1.68 also needs boost_1.67.0_pgi.patch (#9980) 
Its in upstream with the upcoming 1.69 release though.
 2018-12-04 14:49:20 +01:00
George Hartzell
0c3f220fb1 Disallow bcl2fastq2 on OS X (#9966) 
* Disallow bcl2fastq2 on OS X

[Illumina's computing requirements][reqs] claim support for RHEL/CentOS and
go on to say:

> May be possible to install and run on other 64-bit Linux distributions or Unix variants.

The sufficient issue is its reliance of malloc.h.  There may be more.

[reqs]: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/computing-requirements.html

* Add an informative msg for the user
 2018-12-04 13:44:15 +01:00
Neil Flood
e3d204cb8f Expand dependency on qt to allow qt4 (#9964) 2018-12-04 13:37:37 +01:00
Satish Balay
808c2ea5ce petsc: when petsc is built with fortran [default in spack] its best to use hdf5+fortran (#9986) 2018-12-04 13:32:30 +01:00
Neil Flood
47b7016ea7 r-optparse: new package (#9967) 2018-12-04 13:20:08 +01:00
Nick Forrington
9551b34cb5 pgi: Add checksum for PGI 18.10 (#9985) 2018-12-04 13:12:20 +01:00
Matthias Diener
dfb02fd078 cmake: add version 3.13.1 (#9983) 2018-12-04 13:09:49 +01:00
Levi Baber
27e8fcb945 abyss: new version (#9981) 2018-12-04 13:02:36 +01:00
sknigh
a9695bac50 Added missing libtool dependencies to libvterm and unibilium (#10007) 2018-12-04 13:01:37 +01:00
Robert Maynard
0d033a042c Download CMake sources from the Github releases (#10003) 
Now that CMake is providing CMake release artifacts on github,
we should prefer those as they have better download speeds and
uptime.
 2018-12-03 12:35:51 -06:00
jthies
3a2045b7c0 Phist 1.7.4 (#9996) 
* packages/phist: new version 1.7.4 with new variant 'host' to enable/disable host-specific optimizations.
 2018-12-03 09:40:51 -06:00
HAOCHENG LIU
66a62d82c4 Bump vtkm to version 1.3 and add new features (#9968) 
This commit allows users to enable openmp, rendering, logging and mpi
in vtkm. Meanwhile, it adds support for cuda architecture selection.

[VTK-m 1.3 Release notes](https://gitlab.kitware.com/vtk/vtk-m/tags/v1.3.0)
 2018-11-30 19:48:22 -08:00
Mark W. Krentel
cc5446f25c hpctoolkit: overhaul to use spack dependencies (#9946) 
Overhaul hpctoolkit to AutotoolsPackage and to build its dependencies
directly from spack instead of using hpctoolkit-externals.

Remove hpctoolkit-externals since it's no longer needed.
 2018-11-30 18:11:12 -08:00
jwallior
930debcf35 New versions for a few python modules (#9969) 
* py-jupyter-console: Add version 5.2.0

* py-jupyter-core: add version 4.4.0

* py-lxml: add version 4.2.5

* py-zmq: add version 17.1.2

* py-terminado: add version 0.8.1

* py-pexpect: add version 4.6.0

* py-pytables: add version 3.4.4
 2018-11-28 21:44:15 -06:00
Piotr Luszczek
8375b5b571 Add PLASMA version 18.11.0 and Lua variant (#9689) 
* Add PLASMA 18.11.1 with optional Lua and test for headers
 2018-11-28 16:59:05 -06:00
Ondřej Čertík
62f1cf3678 Add f18 package (#9183) 
* Add f18 package

* Fix flake8 errors

* Install the f18 binary into prefix.bin by hand

* Add spack-build into the path

* Fix the license header
 2018-11-28 14:13:30 -06:00
Michael Kuhn
5cea4a75d7 glib: disable SELinux explicitly (#9956) 2018-11-28 10:06:17 +01:00
George Hartzell
e4e980ee97 bcl2fastq2 package: recursively delete after copy (#9959) 
Fixes #9944

73c978d replaced a move with a copy, which cased rmdir to fail (as
it expects an empty directory). This switches to use `shutil.rmtree`
instead.
 2018-11-27 17:22:14 -08:00
Jon Rood
4c3091b05e Fixing problems with lammps dependencies voropp and latte (#9909) 
* Fixing problems with lammps dependencies voropp and latte.

* Always replacing CFLAGS in voropp and specifying voropp+pic dependency in lammps.
 2018-11-27 16:55:21 -07:00
Matthias Diener
2164181d0a git: add version 2.19.2 (#9961) 
Also fixes instructions for new releases
 2018-11-27 16:32:22 -06:00
Neil Flood
8a78c9c6bc Rename py-proj to py-pyproj, consistent with Spack's current naming conventions (#9962) 2018-11-27 16:31:30 -06:00
thelfer
2e04f3daab new package: add support for the tfel package (#9930) 2018-11-27 07:16:55 +01:00
Michael Kuhn
16d3e44515 py-pygobject: add missing pkgconfig dependency (#9955) 2018-11-26 21:41:44 -06:00
Axel Huebl
b26c85301d OpenMPI: Prefer Last 3.X (#9945) 
The latest OpenMPI release, v4.0.0, does not build with many GCC
variants. Since this is our default, a lot of users get hit.

Let's wait for some point releases.
 2018-11-26 16:46:04 -06:00
Eric
20a6dde10b GATK: Add version 4.0.11.0 (#9953) 2018-11-26 14:54:05 -06:00
Eric
d9046e70c1 minced: Add version 0.1.6 (#9951) 2018-11-26 14:22:17 -06:00
Matthias Diener
bab3d7734a hdf5: add version 1.8.21 (#9952) 2018-11-26 12:56:44 -06:00
Michael Kuhn
7df14134c1 go: add 1.11.2 (#9948) 2018-11-26 11:33:55 -06:00
Eric
5cd8233139 metabat: Add version 2.11.2 (#9950) 2018-11-26 11:32:14 -06:00
Miles Perry
28e93a7a79 Feature/gatk (#9872) 
* added 3.8-1 version

* fixed flake8 stuff
 2018-11-26 11:30:21 -06:00
Adam J. Stewart
06dcf72f14 Uncomment dependencies previously disallowed by concretizer (#9942) 2018-11-26 09:11:16 +01:00
Sinan
096922c39d Package/py scikit learn (#9843) 
* add v0.20 specific dependency versions, also add cython and py-test as dependencies

* make flake8 happy

* make cython a build-only dependency
 2018-11-24 19:03:30 -06:00
Neil Flood
4c1733bff4 py-pygresql: new package (#9922) 
* py-pygresql: new package

* Added dependency on py-setuptools, as the build will use it if present
 2018-11-24 17:45:27 -06:00
Neil Flood
e3e01ab3d7 py-psycopg2: new package (#9926) 
* py-psycopg2: new package

* Added dependency on py-setuptools, as the build will use it if present
 2018-11-24 17:45:16 -06:00
Denis Davydov
058a772a52 p4est: fix a typo (#9932) 2018-11-24 17:45:04 -06:00
Matthias Diener
9d2ea84112 mc: add version 4.8.21 (#9943) 2018-11-24 17:42:46 -06:00
Matthias Diener
e86a28aff7 intel-parallel-studio: add missing updates to 2019.1 (#9941) 2018-11-24 15:44:57 -06:00
Neil Flood
9945a59c47 py-geopandas: New package. (#9919) 
* py-geopandas: New package, including packages for its dependencies

* Trailing whitespace removed, etc

* One more trailing whitespace

* Removed some extraneous dependencies. No idea why I thought I needed them, but it now builds fine without them.

* Added a variant +plotting, to include the dependencies required for plotting, as these are large-ish if not being used.

* Added explicit dependency on py-matplotlib
 2018-11-24 15:44:44 -06:00
Matthias Diener
25b9938ad1 cmake: add version 3.13.0 (#9940) 2018-11-24 14:23:10 -06:00
Neil Flood
a0fc573ff4 r-geor: new package, and a couple of its dependencies (#9920) 
* r-geor: new package, and a couple of its dependencies

* Update to new copyright header

* Include the list_url for the R package archive dir

* Added explicit version ranges on dependencies, as per the relevant CRAN pages

* Correct dependency types in r-splancs.
 2018-11-24 14:21:54 -06:00
Andreas Baumbach
862d1799fb new version 18.1 for py-pip (#9938) 
Change-Id: Ie462e802049dd6150767dc555fb5708999e081ec
 2018-11-23 18:09:20 -06:00
Neil Flood
2e510413c3 r-compositions: new package, including its dependencies (#9921) 
* r-compositions: new package, including its dependencies

* Include the list_url for the R package archive dir

* Added explicit version ranges on dependencies, as per the relevant CRAN pages
 2018-11-23 18:06:57 -06:00
Neil Flood
3557b6e149 libspatialite: new package (#9923) 2018-11-22 13:54:52 -06:00
Nicholas Labello
13f2e68688 munge: update versions and url format to reflect switch to .xz format… (#9916) 
* munge: update versions and url format to reflect switch to .xz format in recent releases

* package:munge remove unneeded version-specific urls
 2018-11-22 13:13:40 -06:00
Eric
be92d46962 minced: add version 0.3.2 and fix install paths (#9918) 2018-11-22 13:13:06 -06:00
Neil Flood
c42ceb886c qca: new package (#9924) 2018-11-22 12:45:42 -06:00
Neil Flood
b6e664846a qjson: new package (#9925) 2018-11-22 12:45:17 -06:00
Denis Davydov
0f6f3ece95 p4est: apply patches to 2.0 only (#9928) 2018-11-22 12:40:22 -06:00
Michael Kuhn
f7a445e4b0 multitime: new package (#9929) 2018-11-22 12:39:51 -06:00
Michael Kuhn
ffaf617e74 flecsale: add missing dependencies and fix flecsi runtime model (#9774) 2018-11-22 12:38:59 -06:00
Ken Raffenetti
0eb8cd9a8f Add MPICH version 3.3 (#9915) 2018-11-21 14:42:52 -06:00
Mark W. Krentel
27ad0f1269 dyninst: overhaul package.py to CMakePackage (#9871) 
Drop versions 8.1.x.  These were > 5 years old, no other spack package
uses them, and they used autotools.  Packages 'stat' and 'mitos' still
use 8.2.1, so we keep that.

Switch class Dyninst to CMakePackage.

Clean up how the versions depend on various packages.  For example,
Dyninst used libelf up to 9.2, and then elfutils starting with 9.3.
This makes things easier going forward.

Add variant 'openmp' (default True) to enable openmp support for
ParseAPI.  This was added in 10.0.0.

Add variant 'static' (default False) to also build static libraries.
This goes back to 9.1.0.

Disable cotire for the 9.3.x versions.  Cotire has no real use in a
one-time build and can break parallel builds with both static and
shared libs.
 2018-11-21 10:47:19 -08:00
Elsa Gonsiorowski, PhD
1c5688fcbc correct sha for axl v1.1 (#9907) 2018-11-20 19:28:47 -06:00
Tom Scogland
ba5a251896 package: add asciidoctor gem (#9905) 
* package: add asciidoctor gem

Faster, easier to use, less impossible to install correctly
implementation of asciidoc.

* ritual sacrifice of EOF whitespace to flake8
 2018-11-20 14:32:44 -06:00
Tiziano Müller
84bc1d6654 CP2K related fixes and update (#9308) 
* openblas: enable parallel builds

* cp2k: enable parallel builds

* cp2k: fix building on multilib/Suse distros

use the actual directory path where files where installed to instead of
the default prefix+'/lib'

* cp2k: ensure we have a non-header-only libxsmm

* openblas: disable max num CPU detection on virtualized build

* cp2k: install data and set compiled-in DATA_DIR

* cp2k: make libxc an optional dependency (enabled by default)

* cp2k: link libint statically

* cp2k: declare statically linked library deps as type=build

* cp2k: add support for PGI compiler

* cp2k: rename smm=none to smm=blas for clarification

* cp2k: blacklist unsupported compilers

* cp2k: mark wannier90 a build-time dep since statically linked

* cp2k: make pexsi and elpa optional

* cp2k: add support for v6.1

* libxc: add version 4.2.3

* cp2k: use pkg-config to link properly to libxsmm

* cp2k: fix OpenMP support by making it explicit

Previously, CP2K accepted threaded ELPA or BLAS, leading to #(CPU) processes
being spawned even though no explicit OpenMP was requested. Now the
`popt` variant should truly be thread free while the `psmp` variant uses
threads also internally.

* cp2k: source tarballs moved to GitHub
 2018-11-20 09:23:01 -08:00
dorier
13b95b8ae6 Package: Mercury (#9903) 
* added mercury package

* updating mercury package to satisfy flake8

* improved mercury package
 2018-11-20 11:14:30 -06:00
Jon Rood
128af27c21 Add 2019.1 and 2018.4 version of the Intel performance libraries. (#9899) 
* Add 2019.1 and 2018.4 version of the Intel performance libraries.

* Fixing typo.
 2018-11-20 09:30:53 -06:00
Adam Moody
5127bb590f mpifileutils: add v0.8.1 (#9346) 2018-11-19 20:48:50 -06:00
Michael Kuhn
44d1d928e8 openssl: make 1.1.1 the default version (#9836) 
* openssl: add 1.0.2p, 1.1.0i and 1.1.1

* openssl: make 1.1.1 the default version
 2018-11-19 20:46:38 -06:00
Justin Stanley
7bb9020227 added several new perl modules (#9760) 2018-11-19 20:44:44 -06:00
Justin Stanley
9dfea8ee17 circos: new package starting at 0.69-6 (#9761) 
* circos: new package starting at 0.69-6

* circos: add homepage, simplify paths

* circos: simplified more paths
 2018-11-19 20:44:01 -06:00
Sinan
0a0e5642df gdk-pixbuf: explicitly disable building of gtk-docs (#9882) 2018-11-19 20:42:56 -06:00
Levi Baber
535035b223 r-rrpp: new package (#9887) 2018-11-19 20:42:45 -06:00
Jon Rood
1972376865 Adding openmpi version 4.0.0 (#9888) 2018-11-19 20:42:34 -06:00
Eric
177c5f3c6d breseq: Add version 0.33.1 (#9889) 2018-11-19 20:42:21 -06:00
Sinan
47a641f13b package/harfbuzz: disable building of gtk-docs, add new version (#9891) 2018-11-19 20:42:08 -06:00
Levi Baber
561a561d23 r-crosstalk: remove unnecessary constraint (#9892) 2018-11-19 20:41:41 -06:00
Levi Baber
71943703f2 r-geomorph: new version (#9890) 
* r-geomorph: new version

* r-geomorph: min r version
 2018-11-19 20:41:19 -06:00
Levi Baber
43a26d0850 r-diversitree: new package (#9893) 
* r-diversitree: new package

* r-diversitree: system reqs
 2018-11-19 20:41:01 -06:00
Levi Baber
7e1f96c0aa r-paleotree: new package (#9895) 2018-11-19 20:39:42 -06:00
Sinan
000bb8ca39 package/pango: disable gtk-docs (#9896) 2018-11-19 20:38:52 -06:00
Sinan
71464a8b0a package/gtkplus: disable gtk-docs (#9897) 2018-11-19 20:38:34 -06:00
Mark C. Miller
a6efd22e60 Explicitly set FC= empty for non-fortran builds (#9898) 2018-11-19 20:38:06 -06:00
Eric
0c1988ffdf Trimmomatic: Add version 0.38 (#9883) 2018-11-19 15:56:49 -06:00
Jon Rood
c8a1a81a87 Adding intel-parallel-studio cluster 2019.1 version (#9884) 2018-11-19 15:56:31 -06:00
Daniel Topa
7402112b1f Add UCX v1.4.0 (#9881) 
Verification build
dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack install ucx % gcc @ 4.8.5
==> Installing libsigsegv
==> Installing m4
==> Installing pkgconf
==> Installing ncurses
==> Installing readline
==> Installing gdbm
==> Installing perl
==> Installing autoconf
==> Installing automake
==> Installing libtool
==> Installing numactl
==> Installing zlib
==> Installing openssl
==> Installing diffutils
==> Installing bzip2
==> Installing xz
==> Installing libxml2
==> Installing tar
==> Installing gettext
==> Installing help2man
==> Installing bison
==> Installing flex
==> Installing libnl
==> Installing rdma-core
==> Installing ucx
==> Successfully installed ucx
  Fetch: 1.17s.  Build: 40.59s.  Total: 41.76s.
[+] /scratch/users/dantopa/new-spack/pr.ucx.spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/ucx-1.4.0-ilfonxj2f5my4ur65li3sr7kuvfg3kim

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack spec ucx
Input spec
--------------------------------
ucx

Concretized
--------------------------------
ucx@1.4.0%gcc@4.8.5 arch=linux-centos7-x86_64
    ^numactl@2.0.11%gcc@4.8.5 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-centos7-x86_64
        ^autoconf@2.69%gcc@4.8.5 arch=linux-centos7-x86_64
            ^m4@1.4.18%gcc@4.8.5 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-centos7-x86_64
                ^libsigsegv@2.11%gcc@4.8.5 arch=linux-centos7-x86_64
            ^perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-centos7-x86_64
                ^gdbm@1.18.1%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^readline@7.0%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-centos7-x86_64
                            ^pkgconf@1.5.4%gcc@4.8.5 arch=linux-centos7-x86_64
        ^automake@1.16.1%gcc@4.8.5 arch=linux-centos7-x86_64
        ^libtool@2.4.6%gcc@4.8.5 arch=linux-centos7-x86_64
    ^rdma-core@20%gcc@4.8.5 build_type=RelWithDebInfo arch=linux-centos7-x86_64
        ^cmake@3.12.4%gcc@4.8.5~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-centos7-x86_64
            ^openssl@1.0.2o%gcc@4.8.5+systemcerts arch=linux-centos7-x86_64
                ^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64
        ^libnl@3.3.0%gcc@4.8.5 arch=linux-centos7-x86_64
            ^bison@3.0.5%gcc@4.8.5 arch=linux-centos7-x86_64
                ^diffutils@3.6%gcc@4.8.5 arch=linux-centos7-x86_64
                ^help2man@1.47.4%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^gettext@0.19.8.1%gcc@4.8.5+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-centos7-x86_64
                        ^bzip2@1.0.6%gcc@4.8.5+shared arch=linux-centos7-x86_64
                        ^libxml2@2.9.8%gcc@4.8.5~python arch=linux-centos7-x86_64
                            ^xz@5.2.4%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^tar@1.30%gcc@4.8.5 arch=linux-centos7-x86_64
            ^flex@2.6.3%gcc@4.8.5+lex arch=linux-centos7-x86_64

Environment:
dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ echo $HOSTNAME
darwin-fe2.lanl.gov

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ grep -i 'model name' /proc/cpuinfo | sort | uniq
model name      : Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ lsb_release -d
-bash: lsb_release: command not found

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ uname -a
Linux darwin-fe2.lanl.gov 4.18.8-1.el7.elrepo.x86_64 #1 SMP Sat Sep 15 10:10:09 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ date
Mon Nov 19 10:47:47 MST 2018

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ pwd
/scratch/users/dantopa/new-spack/pr.ucx.spack

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
 2018-11-19 13:20:22 -06:00
Andrea Negri
494d48f012 new package: mongo-cxx-driver (#9880) 
* new package: mongo-cxx-driver

* fixed url
 2018-11-19 13:19:19 -06:00
Eric
36b4758a97 samtools: make zlib/bzip2 dependencies unconditional (#9866) 2018-11-19 10:36:48 -08:00
Andrea Negri
9aa9359604 libmongoc: updated versions (#9877) 2018-11-18 20:35:24 -06:00
Alberto Chiusole
c61250e2ef New package: ecFlow, a work flow manager. (#9867) 
* New package: ecFlow, a work flow manager.

* Fix pep8 style issues.
 2018-11-18 10:13:31 -06:00
Sajid Ali
c45080398c Add +x variant to petsc. (#9830) 
* 	modified:   var/spack/repos/builtin/packages/petsc/package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
 2018-11-17 21:35:37 -06:00
simo-tuomisto
93879e575d mixcr: Added a new package for MiXCR. (#9864) 
* mixcr: Added a new package for MiXCR.

* mixcr: Fixed spack license string.
 2018-11-17 21:19:04 -06:00
Christoph Junghans
26e51ff170 lammps package: added new versions (#9868) 2018-11-16 14:52:26 -08:00
Sinan
22cd6494be py-cython: add new versions (#9846) 2018-11-16 13:20:34 -08:00
Justin Stanley
9dff444570 new package: r-gensa (starting at 1.1.7) (#9858) 2018-11-16 13:13:48 -08:00
Eric
dc2911208f py-ply: fix download url (#9862) 2018-11-16 13:12:05 -08:00
Eric
61adf39fe1 vt package: add zlib dependency (#9870) 2018-11-16 12:52:15 -08:00
Levi Baber
0a57f90d75 r-rgl: update url, add new version (#9796) 2018-11-16 15:26:09 +01:00
Michael Kuhn
c645c8e2a6 py-cffi: add missing pkgconfig dependency (#9784) 2018-11-15 19:38:52 +01:00
Michael Kuhn
d4f8bd5b8d py-cryptography: add 2.3.1 (#9785) 
Required for openssl@1.1 compatibility.
 2018-11-15 18:27:29 +01:00
Michael Kuhn
480951c231 krb5: add missing bison dependency for yacc (#9778) 2018-11-15 17:54:51 +01:00
Michael Kuhn
4d426e63f0 globus-toolkit: add missing pkgconfig dependency (#9775) 2018-11-15 17:54:22 +01:00
Hadrien G
d7983e2aa4 Fix and update verrou (#9847) 
* Fix verrou-python integration

* Add verrou 2.1.0

* Patch level changed in v2.1.0
 2018-11-15 10:22:13 -06:00
Denis Davydov
32884dbc03 dbcsr: minor fixes due to upstream changes (#9799) 2018-11-15 17:10:50 +01:00
Leonhard Reichenbach
2b64047e07 Updated protobuf and py-protobuf to version 3.6.1 (#9536) 
* Updated protobuf and py-protobuf to version 3.6.1

also updated the download link as the repository has moved

* protobuf: modified conflict
 2018-11-15 16:59:04 +01:00
Adam J. Stewart
2723db9f73
Add GMT, CitcomS, and fstrack packages (#9768) 
* Add initial packages for citcoms and dependencies

* Ignore Pythia imports

* Add py-merlin package

* Add GMT package

* Fixes to get GMT working

* Get hc package building

* Get CitcomS 3.2.0 working

* Add fstrack package

* Fix hash
 2018-11-14 23:30:44 -06:00
Levi Baber
b9c50249cf r-cairo: new package (#9794) 
* r-cairo: new package

* Update var/spack/repos/builtin/packages/r-cairo/package.py

Co-Authored-By: baberlevi <baberlevi@gmail.com>
 2018-11-14 21:44:55 -06:00
dorier
8a41cbf813 Argobots: added @develop version and +valgrind variant (#9664) 
* added develop version in argobots package and added valgrind variant

* made autotools required only for develop version

* corrected style

* Added --disable-valgrind

Added --disable-valgrind to explicitly disable it when +valgrind isn't provided.
 2018-11-14 21:39:35 -06:00
Justin Stanley
12177e41f0 r-phytools: new package at 0.6-60 (#9766) 
* r-phytools: new package at 0.6-60

* r-phytools: add list_url

* r-phytools: add deps, dep versions
 2018-11-14 21:39:05 -06:00
Geoffrey Oxberry
605dc8bf85 openblas: add headers property (#9831) 
This commit adds only the public headers from the full list of headers
installed by OpenBLAS; this list of headers is the same as in
netlib-lapack.
 2018-11-14 21:35:42 -06:00
Mark W. Krentel
b53eb2026a elfutils: add version 0.174. (#9812) 
Pass cflags to configure so that configure gets the values from the
spack install line.

Disable -Werror so that we don't fail the build over a stray warning.
 2018-11-14 19:05:08 -06:00
Mark W. Krentel
2554e24d09 libunwind: add version for current snapshot (#9770) 
Libunwind releases are few and far between, so we need access to
recent snapshots from the git repository.

Pass cflags to configure so that make will respect the value from the
spack install line.
 2018-11-14 18:56:52 -06:00
Sergey Kosukhin
75e86a61fe netcdf-fortran: add LDFLAGS to fix contents of libnetcdff.la. (#9647) 2018-11-14 09:40:16 -06:00
Levi Baber
6a08eb88b1 new package: time (#9842) 2018-11-14 09:38:37 -06:00
Michael Kuhn
9a7a532084 node-js: add 10.13.0 and 11.1.0 (#9781) 
Required for openssl@1.1 compatibility.
 2018-11-13 11:39:52 -06:00
Michael Kuhn
e20efb3f8f cmake: add 3.12.4 (#9758) 2018-11-13 11:34:09 -06:00
Michael Kuhn
eddba22e1c perl-net-ssleay: fix build (#9783) 
- Add 1.85
- OPENSSL_PREFIX has to be set in the environment, otherwise Spack's
  openssl will not be found
 2018-11-13 11:30:04 -06:00
Justin Stanley
e1f9ddd574 erne: new package starting at 2.1.1 (#9676) 
* erne: new package starting at 2.1.1

* erne: remove unused configure args

* erne: remove unused prefix arg

* erne: add explicit mpi disable
 2018-11-13 11:02:39 -06:00
Luigi Calori
4f27bb4f4e Fix #9673 : build fonts on powerpc architecture (#9683) 
* use AutotoolsPackage so config.guess get updated by autoreconf step, fix build problem on ppc #9673

* same error, same fix under ppc arch
 2018-11-13 11:01:46 -06:00
Douglas Duckworth
ab48a96149 added r-bindr v 0.1.1 (#9717) 2018-11-13 10:58:31 -06:00
Levi Baber
b668e66b81 r-genomeinfodbdata: url fix (#9732) 2018-11-13 10:57:04 -06:00
Matthias Diener
8b1a5a8e6c intel-parallel-studio: add missing updates (#9742) 
* intel-parallel-studio: add missing updates

* add 2018.4
 2018-11-13 10:56:31 -06:00
Levi Baber
25d71e68f2 Packages/trinotate fix (#9745) 
* trinotate: fix perl location

* trinotate: not where that is

* trinotate: glob

* trinotate: needs perl-dbd-sqlite
 2018-11-13 10:55:59 -06:00
Alberto Chiusole
7938ff9653 Add pic variant to cflags in boost. (#9750) 
* Add pic variant to cflags in boost.

* Improve description in pic variant of boost, see #9750.
 2018-11-13 10:55:01 -06:00
Miles Perry
63535542a1 new version (#9752) 2018-11-13 10:53:47 -06:00
Michael Kuhn
05a4d5a0c6 glib: add 2.56.3 (#9754) 2018-11-13 10:52:56 -06:00
Michael Kuhn
55f8dbbba0 sqlite: add 3.25.3 (#9756) 2018-11-13 10:50:54 -06:00
Michael Kuhn
c7f2c819a1 gdbm: add 1.18.1 (#9757) 2018-11-13 10:50:30 -06:00
Michael Kuhn
52e990dfa1 lmdb: add 0.9.22 (#9759) 2018-11-13 10:49:24 -06:00
Daryl W. Grunau
ff30ab462b eospac version bump (#9763) 2018-11-13 10:47:11 -06:00
Justin Stanley
c26a965c3b r-combinat: new package at 0.0-8 (#9764) 
* r-combinat: new package at 0.0-8

* r-combinat: add list_url
 2018-11-13 10:41:54 -06:00
Michael Kuhn
a852028b02 glib: explicitly disable gtk-doc (#9771) 
glib should not use the globally installed gtk-doc. Otherwise, gtk-doc
can fail with Python errors such as `ImportError: No module named site`.

This is due to the fact that Spack sets `PYTHONHOME`, which can confuse
the global Python installation that is used by gtk-doc.
 2018-11-13 10:37:19 -06:00
Michael Kuhn
fe8c287036 nginx: add 1.15.6 (#9780) 
Needed to compile with gcc@8 and recent versions of glibc.
 2018-11-13 10:25:00 -06:00
Eric
3cd3631fb6 DIAMOND: add version 0.9.22 (#9790) 2018-11-13 10:20:53 -06:00
Eric
4b63b93485 stringtie: add version 1.3.4d (#9791) 2018-11-13 10:20:30 -06:00
Hans Pabst
23c2d5af38 LIBXSMM 1.10 (#9813) 
* LIBXSMM 1.10

* Accurately replaced MD5 with SHA256 sums (libxsmm).
 2018-11-13 10:09:47 -06:00
Eric
fea0722daa aragorn: add version 1.2.36 (#9817) 2018-11-13 10:09:14 -06:00
Eric
5ba76cf908 minimap2: Add versions 2.10 and 2.14 (#9818) 
* Also add missing zlib dependency
 2018-11-13 10:08:42 -06:00
Quinn
2f454c5317 New Package: Nyancat (#9819) 
* nyancat: adding the most important piece of software ever written

* nyancat: some formatting updates

* nyancat: flake8 error fix
 2018-11-13 10:07:54 -06:00
Matthias Diener
6743aef554 charm++: add version 6.9.0 (#9827) 2018-11-13 10:03:22 -06:00
Christoph Junghans
78c7a8218c gromacs: added 2018.[34] (#9828) 2018-11-13 10:02:59 -06:00
Geoffrey Oxberry
f1e5f8e37b hypre: patch only @2.13.0 and @2.14.0 on darwin (#9832) 2018-11-13 09:54:09 -06:00
Michael Kuhn
3f0fc98062 wt: add missing pkgconfig dependency and fix boost version range (#9835) 
wt does not build with newer versions of boost.
 2018-11-13 09:53:44 -06:00
Michael Kuhn
59a6eada53 libssh: fix fetching and add 0.8.5 (#9779) 
Required for openssl@1.1 compatibility.
 2018-11-13 09:51:57 -06:00
Michael Kuhn
68222f2639 libevent: add 2.1.8 and 2.0.22 (#9777) 
- 2.1.8 is required for openssl@1.1 compatibility
- Introduce url_for_version since the URL has changed starting with
  version 2.0.22
 2018-11-13 09:51:26 -06:00
Valentin Clement (バレンタイン クレメン)
1388f6e907 Add new version 1.2.0 to the package (#9837) 2018-11-13 09:49:08 -06:00
Matthias Diener
86b7e6abc3 man-db: add missing gdbm dependency (#9751) 2018-11-13 09:41:43 -06:00
Michael Kuhn
cc928481f8 openssh: add 7.9p1 (#9782) 
- Required for openssl@1.1 compatibility
- Fix openssh's privilege separation path to be below the prefix
 2018-11-13 09:41:17 -06:00
Jon Rood
b4c7ffd424 Adding Paraview version 5.6. (#9788) 2018-11-13 09:36:18 -06:00
Michael Kuhn
86e00e7294 ruby: add 2.5.3 (#9793) 
Required for openssl@1.1 compatibility.
 2018-11-13 09:35:47 -06:00
Michael Kuhn
66ef3c2b18 thrift: add missing pkgconfig dependency (#9834) 
Without pkgconfig, Spack's openssl cannot be found.
 2018-11-13 09:34:51 -06:00
Eric
f48820a71e barrnap package: Add versions 0.6 and 0.7 (#9820) 2018-11-13 09:33:56 -06:00
Phil Tooley
16aa37bdfe New package: openimageio (#9715) 2018-11-13 00:14:29 -06:00
Phil Tooley
ff09fd5a85 New package: dcmtk (#9716) 2018-11-13 00:08:29 -06:00
Michael Kuhn
f56f6d4e38 Fix pkg-config dependencies (#9738) 
Replace dependencies on specific pkgconfig implementation (e.g. pkgconf)
with dependency on pkgconfig virtual package
 2018-11-13 00:01:41 -06:00
Michael Kuhn
077e509dda gplates package: improvements (#9735) 
- Add version 2.1.0
- Now that #9264 has been merged, gplates seems to build fine with newer
  versions of gcc (tested with gcc@8)
- When using the ninja generator, gplates can be built in parallel
 2018-11-12 23:56:59 -06:00
Alberto Chiusole
c7c3fab744 Add 'pic' variant to netcdf packages (#9605) 2018-11-12 23:54:11 -06:00
Peer-Timo Bremer
91302f89e4 TALASS package: replace old version with new version (#9703) 
New version has bug fixes
 2018-11-12 23:38:03 -06:00
Manav Bhatia
0b86675879 libMesh: new version and dependency updates (#9709) 
* added v1.3.1 checksum
* added vtk and petsc variants
* bugfix: enable petsc when slepc variant is specified
 2018-11-12 23:29:58 -06:00
Daniel Topa
79ad078f78 Open MPI: add versions 3.1.3, 3.0.3, update checksums (#9734) 
All checksums are now sha256
 2018-11-12 23:26:39 -06:00
Michael Kuhn
47d74f3bca pkgconf: Add 1.5.4 (#9737) 2018-11-12 23:22:34 -06:00
Matthias Diener
dbdee8e542 chrpath: add new package (#9708) 2018-11-12 23:21:56 -06:00
Phil Tooley
02cdfd654e version/dependency updates for ilmbase and openexr (#9714) 
* include zlib dependency for openexr, fixes #7274
* version bump to openexr/ilmbase 2.3.0
 2018-11-12 23:18:54 -06:00
Cameron Stanavige
230bdce34e new package: flatcc (#9695) 2018-11-12 23:11:52 -06:00
Axel Huebl
152346f275 nlohmann-json: add new version 3.4.0 (#9692) 2018-11-12 23:08:40 -06:00
Ross Miller
7c267e8534 py-numba: update dependencies and versions (#9706) 
The latest version of py-numba (0.40.1) wants a newer version of
py-llvmlite.  Had to add that version to py-llvmlite/package.py.
 2018-11-12 23:07:40 -06:00
Justin Stanley
87df41e0ca migrate: new package starting at 3.6.11 (#9707) 2018-11-12 23:05:54 -06:00
Sinan
9e67216593 new package: PyH5glance (#9700) 2018-11-12 18:55:49 -06:00
Sinan
ec7e5d3b8b new package: python htmlgen (#9699) 2018-11-12 18:47:04 -06:00
Denis Davydov
e04adbca66 gnuplot: add X11 dependency and QT terminal (#9722) 2018-11-12 18:45:27 -06:00
Justin Stanley
553cecaade r-manipulatewidget: new package at 0.10.0 (#9826) 2018-11-12 18:41:03 -06:00
Justin Stanley
2ee0d98be1 r-webshot: new package at 0.5.1 (#9824) 2018-11-12 18:38:48 -06:00
Levi Baber
dcb696bd3f r-callr: adding new dependencies (#9730) 2018-11-12 18:38:03 -06:00
Justin Stanley
5ed3873f2f r-convevol: new package at 1.3 (#9767) 2018-11-12 18:36:31 -06:00
Justin Stanley
8357c1e0bc r-miniui: new package at 0.1.1.1 (#9823) 2018-11-12 18:34:56 -06:00
Justin Stanley
407bfbc2cb r-clustergeneration: new package at 1.3.4 (#9765) 2018-11-12 18:34:03 -06:00
Jim Galarowicz
5dc0b65719 Update Dyninst package file for TBB dependency (#9728) 
* Update Dyninst package file for TBB dependency

Dyninst master and 10.0 release
versions require the tbb package.  This mod
updates the tbb versions adding the one that
dyninst uses and adds the required spack package
changes to dyninst/package.py.

* Put new version of tbb in proper location, per reviewer comment.

* Only depend on tbb if building the development version.

* Changes for the release of Dyninst 10.0.0
 2018-11-09 13:35:11 -08:00
Nichols A. Romero
236b34f3df Introduce fftw-api virtual package for Intel-MKL and FFTW (#9618) 
* Introduce FFTW2 and FFT3 providers for Intel-MKL and FFTW Spack packages.

* make fftw default package for fftw-api virtual package

* virtual package test assertion now provides location of default virtual packages.

* Change name of virtual package to fftw-api and used versioned interface.
 2018-11-09 08:16:11 -08:00
Todd Gamblin
0e60fcccfb utils: merge spack.environment into spack.util.environment 
- `spack.util.environment` is the new home for routines that modify
  environment variables.

- This is to make room for `spack.environment` to contain new routines
  for dealing with spack environments
 2018-11-09 00:31:24 -08:00
Justin Stanley
d1b17e8207 canu: use built-in makefile install (#9726) 2018-11-08 10:28:10 +01:00
Denis Davydov
8f4d6caf32 muparser: minor fixes to 2.2.5 and add 2.2.6 with CMake (#9724) 
* muparser: minor fixes to 2.2.5 and add 2.2.6 with CMake
* dealii: make muparser optional
 2018-11-08 10:05:52 +01:00
Michael Kuhn
da193a07a3 ncl: Add 6.5.0 (#9736) 2018-11-08 10:03:29 +01:00
Levi Baber
55b6105af7
r-delayedarray: new dep in latest vers (#9731) 2018-11-07 10:27:08 -06:00
Valentin Clement (バレンタイン クレメン)
768111c365 Use the raw compiler path for the preprocessing pass in CLAW driver (#9748) 2018-11-07 15:24:24 +01:00
Peter Scheibel
7d97e8b067 New repo for advanced packaging tutorial (#9711) 
* modified tutorial packages

* update hint in hdf5 tutorial file (typo for suggested argument)

* add repo.yaml to tutorial repository

* update tutorial docs to refer user to tutorial package repository

* flake edits

* recommend site scope vs. defaults

* you don't specify the repo's name when adding a repo, just the path
 2018-11-06 19:57:32 -08:00
Levi Baber
4ba3c81bc8
snpeff: add wrapper for SnpSift.jar (#9674) 2018-11-06 08:36:47 -06:00
sknigh
d5327d8d4b Add OpenMPI 3.1.3 and a bug patch (#9680) 2018-11-06 09:12:48 +01:00
Gregory Lee
e6eb2b960e py-backports-functools-lru-cache: add to 'backports' namespace (#9720) 2018-11-05 16:01:03 -08:00
Justin Stanley
d7c9128875 new package: homer (starting at 4.9.1) (#9669) 2018-11-02 18:18:05 -07:00
Eric
b471a3626e freetype: enable-freetype-config build option for 2.9.1 (#9653) 
This builds the 'freetype-config' binary which can be used to get
configuration information about the freetype install, used by some
dependents.
 2018-11-02 18:06:40 -07:00
Tim Law
a33d123e2e Add version 2.0.2 of BookLeaf_Cpp and version 3.0.2 of Typhon. (#9662) 2018-11-02 13:30:52 -07:00
Dmitriy
36ddcc2e97 henson: new package (#9657) 
* henson: new package

* henson: change github path to henson-insitu

* henson: make mpi-wrappers=off by default

* henson: remove unsued variable and spaces to make linter happy

* henson: rename version master to develop
 2018-11-01 18:15:12 +01:00
Thomas Stitt
6a3552274f xeus: new package (#9682) 
* xeus: new package
cppzmq: add version 4.3.0
zeromq: make libsodium optional, on by default

* xeus: add patch so it builds, add new version
nlohmann-json: add more versions
cryptopp: add more versions

* xeus: flake8

* xeus: fix license
 2018-10-31 20:23:44 -07:00
Abhinav Bhatele
939ce40032 ecp-proxy-apps: disable building CANDLE Benchmarks by default (#9691) 
add as a variant
 2018-10-31 12:50:37 -06:00
Federico Ficarelli
383cda2c90 lbzip2: add new package (#9688) 2018-10-31 18:08:00 +01:00
Kelly (KT) Thompson
a3ff21eb2b Provide a newer doxygen version. (#9681) 
* Provide a newer doxygen version.

+ Also provide a patch that allows collaboration diagrams to work properly with
  C++ std::shared_ptr<T>. Ref:
  6c380ba91a
 2018-10-31 18:03:13 +01:00
健美猞猁
79e70afed4 Packmol: a new package. (#9687) 2018-10-31 17:32:09 +01:00
Justin Stanley
abad2c9743 r-dismo: new package starting at 1.1-4 (#9675) 2018-10-31 11:28:09 +01:00
Jim Galarowicz
c10d432a2e Update openspeedshop and cbtf-krell module creation code (#9234) 
* Add the setting of CBTF_MPI_IMPLEMENTATION to the cbtf-krell
  and openspeeedshop package files, so that the mpi implementation
  can be found by the tool.  This allows users to not have to
  set this manually if only one mpi implementation is specified
  in the build.
* Update version ranges for dependencies of cbtf packages
 2018-10-30 18:41:08 -07:00
Ross Miller
718be8a645 Update dependencies for py-llvmlite (#9668) 
Change dependency on llvm from >=6.0 to 6.0:6.99.

Refs #9667
 2018-10-30 21:33:43 +01:00
Alberto Chiusole
f602fd8ea4 New package: RegCM, regional climate model. (#9655) 2018-10-30 13:32:59 -07:00
Axel Huebl
33b65ecca0 GCC: ISL and mpfr upper bounds (#9513) 
* GCC: constrain version 6, 7, and 8 to build with ISL version at
  most 0.18
* GCC version 9 (not yet released) will be compatible with
  ISL version 0.20 so future GCC releases are constrained to build
  with ISL version at most 0.20
* ISL: Add v0.15, replace all md5 sums with sha256 sums for ISL
  versions
* GCC versions before 6 were constrained to build with ISL 0.14
  but have been confirmed to work with ISL 0.15
* GCC: Place an upper bound on GCC's mpfr dependency
 2018-10-30 13:26:41 -07:00
Ruben Di Battista
3c387bfa39 vtk: remove redundant option setting (#9597) 
This eliminates duplicates for a couple options which are set
multiple times.
 2018-10-30 12:47:48 -07:00
Abhinav Bhatele
26bacbcb8c caliper: specify path to libunwind (#9670) 2018-10-30 18:37:44 +01:00