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2018-05-10petsc: specify number of processors used for test case (#8015)David Wootton1-0/+12
For Spectrum MPI, if -np is omitted, the default behavior is to assign one process per process slot, where the default process slot allocation is one per core. On systems with many cores, the number of processes can exceed the size of the grid specified when the testcase is run and the test case fails. This specifies a small number of processes when running the test case to prevent failure.
2018-05-10wireshark: stop cmake from picking up /usr paths (#8053)healther1-2/+14
* stop cmake from picking up /usr paths if spack has corresponding packages Change-Id: I7217122562697c7a642cded2b4bfb606d2e35ffb * add libpcap dependency Change-Id: If0d5c2c94b2c2d1cbb9b19e31e44f870b71ba88b * make cmake actually pick up pcap Change-Id: I67b87fd9282c26f5ff4e0a5aedd8bbbae39a5960 * add libtool build dependency Change-Id: I5c6d14dca7ccbe457318903dd170bb19d004e952 * use .libs for pcap Change-Id: Ibe78f8765524385f9da4a8f9963f2c61632cc9f7 * explicitly add bison build dependency Change-Id: I47112778abdf4c0de81789685a7eca4dddb20f77 * add lua explicitly Change-Id: I8e306e1e4cfa0e16138f3a5109ddcfe912120946 * fix libs usage Change-Id: I8c1e03f10df69e3ef74326a13cacaf0e5498e6aa * add minimal version requirement Change-Id: I4dd181389f9a63067df541b982bc0727f974d4ce
2018-05-09Add new Sundials versions (#8075)David Gardner1-0/+3
* Add new Sundials versions, update minimum cmake version required * specify which versions require a newer cmake * revise cmake dependency * remove develop, add 4.0.0-dev version
2018-05-09Add 3.5.2; Add optional cpp implementation enable for py-protobuf (#8069)mcneish12-0/+17
* Add 3.5.2; Add optional cpp implementation enable for py-protobuf * Make flake8 happy * Give all required install_args
2018-05-09perl-extutils-pkgconfig: Add pkg-config dependency (#8045)Eric1-0/+2
* perl-extutils-pkgconfig: Add pkg-config dependency * perl-extutils-pkgconfig: fix build dependency * perl-extutils-pkgconfig: fix build dependency
2018-05-09llvm+lldb plaform=darwin: check for lldb_codesign certificate (#7012)Geoffrey Oxberry1-0/+20
* llvm+lldb plaform=darwin: check for lldb_codesign Building LLVM with LLDB requires that the "lldb_codesign" code certificate be created (see https://llvm.org/svn/llvm-project/lldb/trunk/docs/code-signing.txt for details). This commit checks for this certificate on Darwin if LLDB is to be built, and returns an informative error message if this certificate is unavailable.
2018-05-08Add gdb@8.1; add optional lzma dependency for debug information support (#8068)mcneish11-1/+4
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 Culpo5-0/+134
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
2018-05-07Specs add a space before dependencies (#7942)Massimiliano Culpo3-26/+45
fixes #7941 Modified string representation of Specs to add a space before deps Unit-tests have been modified accordingly Added a test for regression on #7941
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
2018-05-06Support *.TAR.gz extension. (#7973)健美猫1-1/+1
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
2018-05-05Fix coloring of URLs containing @ symbol (#7799)Adam J. Stewart1-3/+3
* Fix coloring of URLs containing @ symbol * Fix coloring of descriptions containing @ symbol
2018-05-05Change default elf provider on macOS (#7939)Adam J. Stewart1-0/+2
2018-05-05Set default provider for every virtual package (#7784)Adam J. Stewart2-1/+12
* Set default provider for every virtual package * Add unit test to ensure that every virtual package has a default provider explicitly set
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
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