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2019-02-14new variant: simmodsuite for pumi (#8775)Cameron Smith1-1/+25
2019-02-14cp2k is now a MakefilePackage (#10570)Massimiliano Culpo4-251/+269
* cp2k: archive the Makefile after a successful installation * cp2k: all checksums are now sha256 * libint: all checksums are now sha256 + added versions 2.4.X * libxc: all checksums are now sha256 + added version 4.3.2 * cp2k: os.path.join instead of join_path + simplified openmp flags * cp2k: turned into a MakefilePackage * cp2k: refactored edit method so that Makefile writing happens last
2019-02-13pythia6: fix input verification issue and example data checksum. (#10563)Chris Green1-3/+2
* pythia6: fix issue validating integer input. * pythia6: account for apparent update of example data file.
2019-02-13xrootd: allow specification of C++ standard. (#10577)Chris Green1-1/+39
* xrootd: add cxxstd variant. * xrootd: support for recent and upcoming versions.
2019-02-13icu4c: Add cxxstd variant (#10552)Ben Morgan1-0/+15
* icu4c: Add cxxstd variant For versions supported in Spack, ICU4C defaults to the C++11. Provide a variant to default to this, plus options for C++14 and 17 if dependees require for ABI compatibility. * icu4c: cxxstd variant cannot be multi
2019-02-13Add Gaudi and RELAX packages (#9194)Hadrien G3-0/+118
* Add a RELAX package * Add a Gaudi package
2019-02-13Add a DD4hep package (#9208)Hadrien G1-0/+43
2019-02-13Add new ROOT release, move to SHA-256 checksums (#10583)Hadrien G1-13/+15
2019-02-13Updated Geant4 and dependencies clhep and vecgeom to use cxxstd= variant ↵Patrick Gartung17-50/+509
(#10518) * Updated Geant4 and dependencies clhep and vecgeom to use cxxstd= variant so that it is applied consistently. * Make standalone geant4 data packages that are used when data is not installed with geant4. This allows installing the data files are externals that can be common to many compiler version. * move geant4 data package dependencies to umbrella package geant4-data
2019-02-13Dynamic library/include paths (#8136)Peter Scheibel1-4/+0
Fixes #7855 Closes #8070 Closes #2645 When searching for library directories (e.g. to add "-L" arguments to the compiler wrapper) Spack was only trying the "lib/" and "lib64/" directories for each dependency install prefix; this missed cases where packages would install libraries to subdirectories and also was not customizable. This PR makes use of the ".headers" and ".libs" properties for more-advanced location of header/library directories. Since packages can override the default behavior of ".headers" and ".libs", it also allows package writers to customize. The following environment variables which used to be set by Spack for a package build have been removed: * Remove SPACK_PREFIX and SPACK_DEPENDENCIES environment variables as they are no-longer used * Remove SPACK_INSTALL environment variable: it was not used before this PR
2019-02-13add latest version of pixman (#10580)Peter Doak1-2/+3
2019-02-13Eigen package: deactivate some dependencies (#10572)Hadrien G1-7/+10
Set defaults in eigen package to omit typically-unused dependencies
2019-02-13Update lbann sw stack dependencies (#10579)Brian Van Essen3-8/+5
* Added a package for the MDAnalysis toolkit. * Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI even when using CUDA. Fixed small bugs within both LBANN and Hydrogen packages. Added requirements for breathe and cereal to LBANN. * Update use case for doc dependencies. * Cleaning up some of the LBANN software stack dependencies.
2019-02-13Cnvnator: a new package. (#8959)健美猞猁1-0/+50
2019-02-12casacore: new package (#7471)健美猞猁1-0/+71
2019-02-12xerces-c: Add cxxstd variant (#10561)Ben Morgan1-0/+15
Add variant to support compiling against main C++ standards if needed for ABI compatibility. Use 'default' value as Xerces-C autoconf system does not enforce a minimum, or set a default, C++ standard.
2019-02-12lbann: updated versions (#10568)Brian Van Essen3-0/+7
2019-02-12remove remaining lzma dependencies (#10553)Matthias Diener2-2/+1
2019-02-12openssl: add version 1.1.1a (#10562)Matthias Diener1-0/+1
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/).
2019-02-08Adding 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.
2019-02-07netlib-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)
2019-02-07petsc: 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
2019-02-06mafft 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>
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