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7695 Commits

Author SHA1 Message Date
Levi Baber
1a34bebe79 genemark et package: add version 4.38 (#10519) 
Also add heu_dir to bin/
 2019-02-06 13:46:35 -06:00
Jon Rood
11c52c3bf7 Paraview package: update PYTHONPATH for dependents (#10501) 
Add vtkmodules directory to PYTHONPATH in Paraview for Trilinos
 2019-02-06 12:45:14 -06:00
Daniel Topa
d9d75635c7 Add Python 3.7.2 updated (#10531) 
Also add versions 3.7.1, 3.6.8, 3.6.7, 3.6.6. Does NOT alter preferred version (2.7.15).

Supplants PR 10491 "Add Python 3.7.2" (https://github.com/spack/spack/pull/10491).

Verification builds on LANL Darwin:

**Intel Xeon**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.2-d3p7vg6w2r563cpmwsmbgjbsiqc4j4fq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.1-ibom6qj2z64egyaqz5htkwp5tr362il6
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.8-rkifc3c7mjgdglw27upiap767ut4wpkz
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.7-meuesn43twttt756exyzqgdhohjgipjq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.6-qwnwme7otyuoqqudcglfmfy75t5npywl

**Arm**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.2-qj27kzs4ttdqudm3hsi3pt57kv7lshco
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.1-io5eneirgvpegy3tosvp6wq5ndf7yjis
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.8-ej3vnvta2hbtrh7p5hokfqkuewxeqgsa
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.7-l3qnue72ewppn2wxza3w6l62l7ijlque
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.6-b55pdoqsr5bie4k5djd4vokm3nywhm45

**Power9**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.2-cicayvl7ki4tswoqlljsmcetwqcnoh3x
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.1-7vej3zvnvyj2jvz5lnxhnts3ok2fcxbp
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.8-xijljmdanyrybcx2rv65qshycmbrfv6c
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.7-vqdhzg7c3xxxregqmzxsqqfzxt2hajvq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.6-jf4bnsdwk3qjhtmvjjhblnrcz5dztfdq

2019-02-05
Signed-off-by: Daniel Topa <dantopa@lanl.gov>

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
 2019-02-06 12:03:25 -06:00
Valentin Clement (バレンタイン クレメン)
548e6736c4 Update CLAW package with version 1.2.1 (#10528) 2019-02-06 15:51:52 +01:00
Levi Baber
881ce3a5c2 perl-yaml: new package (#10514) 2019-02-06 15:47:54 +01:00
simo-tuomisto
1be258a587 wordnet: new package (#10526) 2019-02-06 15:38:48 +01:00
Denis Davydov
871e7f525c xsdk: enable slepc in deal.ii (used to be a concretization error) (#10218) 2019-02-06 07:59:36 -06:00
Phil Carns
0b4a7dd04a New package: PMDK (#10453) 2019-02-05 16:53:16 -06:00
Justin Stanley
003ebf8bab r-wgcna: new package at 1.64-1 (#10392) 2019-02-05 09:00:25 -06:00
Axel Huebl
293e5c0781 MPark: Variant v1.4.0 (#10512) 
Add the latest release of Michael Park's C++ Variant lib.
 2019-02-05 15:18:19 +01:00
Phil Carns
de91d0badc mercury package: add 'udreg' variant (#10415) 
Faster and/or more robust in some cases on Cray platforms
 2019-02-04 19:51:04 -06:00
Levi Baber
c7ecb66a2f New package: perl-hash-merge (#10506) 2019-02-04 18:05:36 -06:00
Levi Baber
736a317e0c New package: perl-clone-choose (#10507) 2019-02-04 18:04:55 -06:00
Christoph Junghans
514cf0c1f4 votca*: add v1.5 (#10495) 
* votca-tools: add v1.5

* votca-csg: add v1.5

* votca-xtp: add v1.5

* votca-ctp: add v1.5
 2019-02-04 12:57:19 -07:00
Justin Stanley
478c3f5e8b augustus: fix bam2wig auxprog build (#10362) 
* augustus: fix bam2wig auxprog build

* augustus: few more changes to make new versions work
 2019-02-04 10:36:10 -06:00
Matthias Diener
bca72036a8 tar: add version 1.31 (#10485) 2019-02-04 11:02:13 +01:00
Axel Huebl
17cc4f208f Catch2: v2.6.0 (#10490) 
Add the latest Catch2 release.
 2019-02-04 10:52:47 +01:00
wspear
43fae5b807 New package: py-alembic (#10436) 2019-02-01 16:24:44 -06:00
wspear
ec7c7332c0 New package: py-prometheus-client (#10440) 2019-02-01 16:23:59 -06:00
Nicholas Labello
8c87a937e1 plumed package: add versions 2.4.4 and 2.5.0 (#10496) 2019-02-01 16:21:55 -06:00
Mark W. Krentel
a1969d9eec dyninst: add patch to work with new boost (#10454) 
Add tribool.patch to add explicit casts from tribool to bool in two
places.  Boost, starting with version 1.69, turned on explicit
conversions for tribool, which breaks the build for dyninst.

This is merged into the current dyninst develop and is expected to be
part of the next release, so the version range uses the current
release as an upper bound.
 2019-02-01 16:18:16 -06:00
wspear
c2b06c27ac New package: py-async-generator (#10439) 2019-02-01 12:40:19 -06:00
zschulte
a701c412bc gatk package: new versions, updated helper script (#10459) 
Closes #10168

* Add versions 4.1.0.0 and 4.0.12.0
* Replace md5 checksums with sha256
* Logic to generate a helper script for versions earlier than 4 was
  not running. This corrects the branch which controls whether this
  script is generated.
* Constrain Java dependency to version 8 (GATK does not work with
  Java 11)
* Avoid adding scripts that have dependencies not handled by Spack
  such as gcloud and google-chrome. These scripts are good candidates
  for later extensions.
 2019-01-31 16:10:06 -06:00
Ricardo Silva
cf754245fd py-pybigwig: fix build with python3, add numpy variant (#10444) 
* added patch to correctly pick up non-system curl when building
  with Python 3
* added numpy variant
* add version 0.3.12
* update checksums to sha256
 2019-01-31 14:50:10 -06:00
snehring
21afd258a4 New package: openjdk (#9861) 
Closes #2622

This retrieves and installs the binary of Oracle's OpenJDK (an
open-source JDK implementation). The logic is largely based on the
Spack JDK package (Oracle's closed-source JDK implementation).

For now this is only supports Linux. If the download could be
customized based on OS (for the same version), binaries are also
available for MacOS and Windows.
 2019-01-31 12:54:28 -06:00
Matthias Diener
ec78d362d2 git-lfs: add version 2.6.1, update build system (#10405) 
Build system was changed to use a Makefile. Therefore older versions
(which don't support this) are removed. The new build system also
supports testing by default.
 2019-01-30 21:21:08 -06:00
Tom Payerle
c42528fac2 fftw: fix include error for 2.x versions (#10039) 
Fixes #7372

Added patch method which renames config.h in the fftw subdir of the
source tree. fftw 2.1.5 appears to ship with a copy of this file
with all defines commented out. This gets read by the #include
directives instead of the version in the build directory with the
correct defines. As a result, many C preprocessor macros left
undefined, including F77_FUNC_ which causes the bulk of fttwf77.c
to be skipped due to an #ifdef, so fftw_reverse_int_array et al
not included in library. Fixes #7372

Also fixed some inconsistencies with the handling of quad and
long_double in specs between the configure method and the build,
check, and install methods.
 2019-01-30 21:18:10 -06:00
Axel Huebl
2aad75d98f HDF5: Add develop Version (#10382) 2019-01-30 21:04:24 -06:00
Phil Carns
36c46a7daf Mercury package: update libfabric dependency on Cray (#10408) 
The Mercury package previously depended on libfabric@develop on
Cray platforms in order to pick up a fix for the GNI provider that
was only available in git. This is no longer needed now that the
libfabric package is at 1.7.0.
 2019-01-30 20:57:31 -06:00
Justin Stanley
5a431eb408 r-pkgmaker: add 0.27, new dependencies (#10419) 2019-01-30 20:54:24 -06:00
Michael Kuhn
b1af6b43dc gobject-introspection: add 1.56.1 and fix download (#10462) 
Define url_for_version, since Spack's default substitution is
not sufficient
 2019-01-30 20:53:08 -06:00
Matthias Diener
3ce0fba036 go: fix directory structure issue for 1.11.5 (#10484) 2019-01-30 20:30:05 -06:00
Chuck Atkins
be38fded9b cmake: Fix linker errors on Darwin when using external dependencies (#10467) 
Adds upstream patch for a missing framework. This is anticipated
to be fixed by CMake 3.13.4 so is only applied up to version 3.13.3
 2019-01-30 20:24:20 -06:00
Matt Belhorn
2b6bf06150 libsodium: Updates source URL. (#10483) 
The source URL for versions 1.0.15 and older is updated to reflect where
those archives are now hosted by the upstream libsodium developers.
 2019-01-30 20:14:41 -06:00
Jon Rood
86747b39d4 ninja: Add kitware version with fortran capability (#10470) 2019-01-30 20:06:09 -06:00
G-Ragghianti
9630d732d6 New package: SLATE (#10434) 2019-01-30 19:59:26 -06:00
Jason Lee
c698384216 jemalloc: Add variant to prepend public api with "je_" prefix (#10356) 2019-01-30 19:16:33 -06:00
Justin Stanley
993745b919 redundans: add 0.14a (#10006) 
Also update install to use globbing
 2019-01-30 18:55:59 -06:00
Samuel Thibault
9bfcbcc155 New package: simgrid (#10076) 2019-01-30 18:39:59 -06:00
Cameron Smith
9d7f215e47 zoltan: detect metis int64 variant (#10051) 
Configure zoltan depending on metis int64 support
 2019-01-30 15:19:38 -06:00
dorier
477d3fb479 Package py-keras: add new versions and dependencies (#10353) 
Add new versions for py-keras. Versions of py-keras at or after
2.2.0 require keras-processing and keras-applications packages.
Add these packages to Spack and add dependencies to the py-keras
package.
 2019-01-30 14:32:37 -06:00
Jimmy Tang
47887499bf cudnn package: add version 7.2 (#10481) 2019-01-30 13:44:24 -06:00
sknigh
d4fbaa054f Update opa-psm2 package (#10344) 
* Add version 11.2.68
* Add variant to disable AVX2 for older hardware
* Change the makefile so libraries and includes are not placed
  under $PREFIX/usr
* Updated URL and homepage
 2019-01-30 13:38:48 -06:00
Justin Stanley
a3926620ee r-preprocesscore: add version 1.44.0 (#10389) 2019-01-30 13:30:06 -06:00
Justin Stanley
65429026af r-impute: add version 1.56.0 (#10390) 2019-01-30 13:29:09 -06:00
Abhinav Bhatele
5c99716160 codes package: add version 1.1.0 (#10414) 2019-01-30 13:27:56 -06:00
Justin Stanley
25d2ccfcc5 r-runit: new package at 0.4.32 (#10416) 2019-01-30 13:26:34 -06:00
Justin Stanley
2a28e6e6bb r-bibtex: new package at 0.4.2 (#10417) 2019-01-30 13:25:43 -06:00
Justin Stanley
9efeff6b1f r-rngtools: add 1.3.1 (#10418) 2019-01-30 13:25:10 -06:00
Abhinav Bhatele
16819a5b18 ROSS package: update homepage and git url (#10429) 2019-01-30 13:24:14 -06:00