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2019-02-08work around an issue with docker/dockerhub (#10547)Omar Padron1-0/+14
* try to workaround an issue with docker/dockerhub * apply workaround only when running in travis
2019-02-08root package major update (#8428)Javier Cervantes1-51/+416
* Extend current recipe for root package * Add removed old version * Add dependency type for Python and R packages * Add compiler variants * Adding new root version: 6.14.00 * Add back the minimum cmake version required * LZ4 and xxhash support for old (using builtin options) and new versions (external packages) * Set PYTHONPATH in setup_environment * Address typos and issues pointed by HadrienG2 * Add newer ROOT versions * Solve support for asimage * Define incompatible variants * Organize old dependencies * Add support for minuit * Add support for pythia6 * Remove unneeded list_url * Update license header * Remove block of commented old dependencies * Contrain Qt version * Comment pythia8 variant/dependency, not supported by spack * Force not to build pythia8
2019-02-08libarchive: remove lzma dependency (#10517)Matthias Diener1-1/+0
lzma was last updated in 2008 and has compilation issues on some platforms. The format has been superceded by xz (see e.g. https://tukaani.org/xz/).
2019-02-08CudaPackage: fix wrong version range (#10551)Denis Davydov1-1/+1
2019-02-08Adding a package for cardioid. (#10448)Robert Blake1-0/+72
* Adding a package for cardioid. * Changing package to pass flake8 * Removing template leftovers per @ax3l 's advice * Adding a homepage so tests pass. * Removing whitespace for flake8 * Changing the name of master branch to match spack standards.
2019-02-08meson: add 0.49.1 and disable rpath stripping (#10463)Michael Kuhn2-0/+17
rpath stripping breaks (at least) the gtkplus build because at-spi2-atk's dependencies can not be found.
2019-02-07bug report template: suggest --stacktrace instead of -s (#10548)Peter Scheibel1-4/+4
1137b18 removed the -s option from spack such that to see a stack trace you must pass the --stacktrace option. The bug report templates were not updated accordingly.
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
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