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2018-05-08opencv updates for lbann (#6502)Brian Van Essen2-32/+122
Add variants to control building of many 3rd-party modules in opencv. They are enabled by default, which matches the defaults chosen by opencv when these options are not set explicitly. This also updates the lbann opencv dependency to disable most of these new variants by default in order to build faster.
2018-05-08Packages can tune the list of files to be archived at the end of install (#7760)Massimiliano Culpo1-0/+53
Fixes #2781 This PR introduces a new attribute for packages called `archive_files`, which designates files that should be saved from a package build (e.g. the config.log generated during autotools builds). The attribute contains a list of glob expressions; Any file that matches will be archived in the `<prefix>/.spack/archived-files` directory. Errors that occur when archiving files are collected and reported in a file named `<prefix>/.spack/archived-files/errors.txt`. `AutotoolsPackage` and `CMakePackage` provide a sensible default override for this attribute.
2018-05-08Py cnvkit: updating dependencies (#8057)peetsv1-1/+3
* py-pyfaidx: adding new package * updating the url * identifying dependencies
2018-05-08intltool requires patching for newer perl versions (#8061)Gregory Lee1-0/+6
2018-05-08added stat version 4.0.0 (#8062)Gregory Lee1-0/+2
2018-05-08added shared-mime-info version 1.9 (#8063)Gregory Lee1-0/+1
2018-05-08Updates to Google Benchmark package: (#8056)Andrew Gaspar1-0/+10
- Adds v1.3.0 and v1.4.0 - List explicit CMake version dependency (from Benchmark CMake files) - Disable the building of tests. Starting in v1.4.0 this introduced a dependency on GoogleTest Tested by building all versions on macOS High Sierra
2018-05-08Fix superlu-dist with PETSc 3.9.0 (#8048)Ce Qin1-2/+2
2018-05-08pybind11: v2.2.3 (#8051)Axel Huebl1-0/+6
* pybind11: 2.2.3 new release for pybind11, v.2.2.3: https://github.com/pybind/pybind11/blob/v2.2.3/docs/changelog.rst#v223-april-29-2018 * pybind11: compiler support mark older versions as conflicts
2018-05-08googletest: add variant to enable/disable threads (#8052)Geoffrey Oxberry1-0/+6
Add Google Test variant to enable/disable building with threads.
2018-05-08openmpi: new version (#8055)Levi Baber1-1/+2
2018-05-07r-genie3: new package (#8044)Yifan Zhu1-0/+38
2018-05-07manta: Create new package (#8043)Eric1-0/+41
* manta: Create new package * manta: Create new package * manta: fix dependency types
2018-05-07py-pysqlite: Create new package (#8042)Eric1-0/+37
2018-05-07perl: add 5.26.2 (#7984)Denis Davydov1-7/+10
* perl: add 5.26.2 * perl: add 5.22.4 * move Misc releases to EOL
2018-05-07pkgconf: use alpine linux mirror to avoid ssl error (#8039)Christoph Junghans1-1/+1
2018-05-07Add patch (#8034)anne-glerum2-0/+35
2018-05-07trilinos: minor cleanup (#7987)Andrey Prokopenko1-96/+115
2018-05-07py-dlcpar: Add package description (#8032)Eric1-1/+2
2018-05-06add opencv 3.4.1 (#8031)Stephen McDowell1-0/+1
2018-05-06metabat: Create new package (#7991)Eric1-0/+54
* metabat: Create new package * fix Perl script shebangs and BOOST_ROOT environment * add perl script fix function * add perl dependency and fix positional argument for Python 2.6
2018-05-06Add package wireshark and dependencies (#8024)healther3-0/+210
* add wireshark Change-Id: I1ef674ff286db2e06baaf9fca65982d1145cfa79 * fix qt4 build Change-Id: Ieb9989b9fec1a0e02388197f971ee66b591d45c5 * remove commented lines Change-Id: Ia67bfaf1beba06dd710cee56aec06bc36b293d34 * flake8 fix Change-Id: Ica1b2cce2be2faca82a4177c3cdc3a0bb005c031 * remove clutter Change-Id: I6061fe56a88f8c7b7e03fdce5e3eae04036ad2d8 * fix dependencies Change-Id: I8160c70c9333c9f5e82ed5fc73633455df568972 * use dot syntax instead of join_path Change-Id: Id1f737299b603fa4093b58571d46a64b0dd84895
2018-05-06macOS-specific patch no longer applies to GCC 8 (#8029)Adam J. Stewart1-1/+1
2018-05-05py-udunits: New package (#7998)Elizabeth Fischer1-0/+69
* py-udunits: update * Use standard py-netcdf4 * Remove unnecssary import? * Suggested simplifications * flake8
2018-05-05A new library: libshm. (#8028)健美猫1-0/+38
2018-05-04Bump pysam to 0.14.1. (#7988)健美猫1-1/+7
* py-pysam requires curl. * py-pysam conflicts with htslib@1.7. * Bump py-pysam versions. * Add more dependencies.
2018-05-04Added GCC 8.1.0 (#8026)sknigh1-0/+1
Built once on Centos 7 w/ external GCC 4.8.5 compiler
2018-05-04a new package: papyrus. (#8023)Jungwon Kim1-0/+38
* a new package: papyrus. * removed the empty cmake_args * changed md5 checksum for v1.0.0 * make a long line short * one long line url
2018-05-04Bump samtools, hstlib and bcftools to version 1.8. (#8020)健美猫3-0/+7
* Bump samtools and hstlib to version 1.8. * rm .bak. * Bump bcftools to 1.8. * bcftools@1.8 depends on libzip.
2018-05-04py-more-itertools: new package (#8004)Elizabeth Fischer1-0/+38
* py-more-itertools: new package * code review
2018-05-04Hic-Pro: fix a typo and replace hard-coded version. (#8022)健美猫1-2/+2
* Fix a typo and replace hard-coded version. * version -> self.version.
2018-05-04openmpi: don't build static libraries if slurm is activated (#8021)Massimiliano Culpo1-1/+9
According to this comment: https://github.com/open-mpi/ompi/issues/4338#issuecomment-383982008 on an OpenMPI issue, using `--enable-static` silently disable slurm support.
2018-05-03gdal: update (#8008)Elizabeth Fischer1-4/+9
* gdal: update * Remove unneeded depends(python)
2018-05-03Bump r-rcpp versions. (#8016)健美猫1-0/+2
2018-05-03pism: new package (#8010)Elizabeth Fischer1-0/+171
* pism: new package * Implement code review * Remove pointless docstring5 * Fixed missing trailing quote
2018-05-03py-numpy: update (#8003)Elizabeth Fischer2-4/+9
* py-numpy: update * Better constrain when can / cannot parallel build. * Update SciPy parallel logic to be specific to Python 3.5+, same as in Numpy.
2018-05-03py-bsddb3: update (#8006)Elizabeth Fischer1-1/+5
* py-bsddb3: update * Change py-setuptools to build dependency
2018-05-03pfunit: update (#7994)Elizabeth Fischer1-12/+15
2018-05-03Everytrace: update (#7995)Elizabeth Fischer1-3/+7
2018-05-03py-yamlreader: new package (#7997)Elizabeth Fischer1-0/+39
2018-05-03gmp: update (#7999)Elizabeth Fischer1-0/+2
2018-05-03py-scipy: update (#8000)Elizabeth Fischer1-4/+1
2018-05-03py-pyside: update (#8002)Elizabeth Fischer1-0/+14
2018-05-03py-cython: update (#8005)Elizabeth Fischer1-0/+5
2018-05-03genomefinisher: Create new package (#7989)Eric2-0/+65
2018-05-03 py-crispresso: Create new package (#7990)Eric1-0/+46
* py-crispresso: Create new package * py-crispresso: Create new package
2018-05-03New Package: ruby-svn2git (#7979)Kelly (KT) Thompson1-0/+48
* New Package: svn2git https://github.com/nirvdrum/svn2git svn2git is a tiny utility for migrating projects from Subversion to Git while keeping the trunk, branches and tags where they should be. It uses git-svn to clone an svn repository and does some clean-up to make sure branches and tags are imported in a meaningful way, and that the code checked into master ends up being what's currently in your svn trunk rather than whichever svn branch your last commit was in. * Actually requires +perl variant of subversion. * fix style issue.
2018-05-03A new package: nanopb. (#7981)健美猫1-0/+38
* A new package: nanopb. * flake8. * Remove py-pytorch.
2018-05-03Bump pgi to 18.4. (#7980)健美猫1-0/+1
* Bump pgi to 18.4. * Remove the empty line. * Update.
2018-05-03Bump gatk version to 4.0.4.0. (#7985)健美猫1-5/+13
* Bump gatk version to 4.0.4.0. * Update. * Fixed. * Fixed.
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