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Author SHA1 Message Date
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