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2019-02-07netlib-scalapack package: add CMake test patch (#10452)Piotr Luszczek2-0/+46
Add patch to fix Fortran mangling in CMake test This is a fix for builds with GCC 6/7/8 and CMake 2/3. It includes a link to the issue where this is reported. For now, the Spack package applies the patch to all releases >= 2.0.2
2019-02-07repeatmasker package: add variant for cross_match engine (#10534)Justin Stanley1-1/+13
2019-02-07New package: py-jupyterhub (#10461)wspear1-0/+31
This package depends on both python 3.5+ and node-js which depends on python 2.7/2.8 to build. Currently it can only be installed if the node-js package's python dependency is manually removed, so node-js will build with python found on the system rather than provided by spack. Upcoming commits may allow spack to reconcile this automatically.
2019-02-07mirdeep2 package: make sure bins are executable (#10515)Justin Stanley1-0/+2
2019-02-07Trilinos package: update superlu-dist dependency (#10511)mathsen1-1/+1
Trilinos master branch gets the latest superlu-dist (currently 6.1.0)
2019-02-07log-parse: fix error message when no error lines are found (#10543)Massimiliano Culpo1-1/+1
2019-02-07petsc: petscvariables is used from user makefiles - so it should not have ↵Satish Balay1-0/+4
spack compilers listed (#10365)
2019-02-07petsc4py and libensemble: add @develop dependencies (#10539)Satish Balay2-0/+4
* py-petsc4py: add @develop * py-libensemble: add @develop dependency on py-petsc4py@develop
2019-02-07petsc@xsdk-0.2.0: fix sowing dependency (#10535)Satish Balay1-0/+1
2019-02-07xsdk@develop fixes (#10521)Satish Balay2-4/+9
* xsdk@develop: switch trilinos from @master to @develop * xsdk@develop: dtk - fix trilinos dependency on dtk. - dkt-3.0 should be used with trilinos-12.4* - dtk/master should be used with trilinos@develop
2019-02-07orthofiller: new package at 1.1.4 (#10373)Justin Stanley1-0/+38
2019-02-07fixed checksum (#10393)Gregory Lee1-1/+1
2019-02-07new package: perl logger simple (#10509)Levi Baber1-0/+17
2019-02-07perl-file-homedir: new package (#10533)Levi Baber1-0/+17
2019-02-07py-biopython: new version (#10532)Levi Baber1-0/+2
2019-02-07cmake: add version 3.13.4 (#10538)Matthias Diener1-0/+1
2019-02-06phrap-crossmatch-swat: new package at 1.090518 (#10529)Justin Stanley1-0/+25
2019-02-06Add x86_64 as target to cray platform (#10369)Mario Melara1-0/+4
Add x86_64 as a target for the Cray platform, and also designate it as the default front_end target.
2019-02-06mafft package: add version 7.407 (#10488)Owen Solberg1-0/+1
2019-02-06jdk package: add version 1.8.0_202 (#10536)Matthias Diener1-0/+2
2019-02-06New package: perl-object-insideout (#10508)Levi Baber1-0/+20
2019-02-06fmt package: fix cmake arguments (#10500)Matthias Wolf1-1/+1
2019-02-06py-black: add new packageStephen Herbein1-0/+29
2019-02-06py-toml: add latest version and update checksums to sha256Stephen Herbein1-1/+2
A version >= 0.9.4 required for py-black. Added latest, which is 0.10.0. Manually verified that the .tar.gz for v0.9.3 used to generate the sha256 matched the previous md5.
2019-02-06curl package: add version 7.63.0 (#10516)Matthias Diener1-0/+1
2019-02-06py-multiqc: add version 1.7 (#10520)Douglas Duckworth1-4/+5
Added sha256 for py-multiqc as well as require py-matplotlib < v 3.0
2019-02-06genemark et package: add version 4.38 (#10519)Levi Baber1-1/+9
Also add heu_dir to bin/
2019-02-06Paraview package: update PYTHONPATH for dependents (#10501)Jon Rood1-2/+7
Add vtkmodules directory to PYTHONPATH in Paraview for Trilinos
2019-02-06Add Python 3.7.2 updated (#10531)Daniel Topa1-1/+6
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>
2019-02-06CUDA compiler conflicts for Linux (#10460)Nichols A. Romero1-14/+69
* CUDA compiler conflicts for Linux. * Add Volta and Turing GPUs. * Add mandatory conflict for Volta and Turing GPUs. * Revert "CUDA compiler conflicts for Linux." This reverts commit 7d4ff654ac53aad272c59e9f7f8bb3fbb32bcec4. * Compiler conflicts introduced from previous commit into CUDA packaged moved and integrated into CUDA build system. * More conversative with compiler conflicts for cuda 10.0.130, since I don't know what will happen with future cuda 10.x releases. * Correct off-by-one errors in clang conflicts for x86_64 Linux. * No restrictions on Apple Clang compiler until we are able to distinguish Xcode clang from github clang more easily. Note to fix this in the future. * Change comment to clarify that github clang refers to LLVM clang. * Fix and simplify index range. * Fix overlapping conflicts for CUDA 10.0.130 * Removed extra ^cuda from conflict.
2019-02-06Update CLAW package with version 1.2.1 (#10528)Valentin Clement (バレンタイン クレメン)1-0/+1
2019-02-06perl-yaml: new package (#10514)Levi Baber1-0/+17
2019-02-06wordnet: new package (#10526)simo-tuomisto1-0/+33
2019-02-06xsdk: enable slepc in deal.ii (used to be a concretization error) (#10218)Denis Davydov1-2/+2
2019-02-05New package: PMDK (#10453)Phil Carns2-0/+75
2019-02-05r-wgcna: new package at 1.64-1 (#10392)Justin Stanley1-0/+31
2019-02-05MPark: Variant v1.4.0 (#10512)Axel Huebl1-1/+2
Add the latest release of Michael Park's C++ Variant lib.
2019-02-04mercury package: add 'udreg' variant (#10415)Phil Carns1-0/+10
Faster and/or more robust in some cases on Cray platforms
2019-02-04New package: perl-hash-merge (#10506)Levi Baber1-0/+18
2019-02-04New package: perl-clone-choose (#10507)Levi Baber1-0/+16
2019-02-04votca*: add v1.5 (#10495)Christoph Junghans4-10/+15
* votca-tools: add v1.5 * votca-csg: add v1.5 * votca-xtp: add v1.5 * votca-ctp: add v1.5
2019-02-04augustus: fix bam2wig auxprog build (#10362)Justin Stanley1-5/+35
* augustus: fix bam2wig auxprog build * augustus: few more changes to make new versions work
2019-02-04tar: add version 1.31 (#10485)Matthias Diener1-0/+1
2019-02-04Catch2: v2.6.0 (#10490)Axel Huebl1-0/+1
Add the latest Catch2 release.
2019-02-01New package: py-alembic (#10436)wspear1-0/+17
2019-02-01New package: py-prometheus-client (#10440)wspear1-0/+17
2019-02-01plumed package: add versions 2.4.4 and 2.5.0 (#10496)Nicholas Labello1-1/+3
2019-02-01dyninst: add patch to work with new boost (#10454)Mark W. Krentel2-0/+35
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.
2019-02-01New package: py-async-generator (#10439)wspear1-0/+18
2019-01-31gatk package: new versions, updated helper script (#10459)zschulte1-44/+76
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.
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