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2019-03-13revbayes: new version (#10873)Levi Baber1-2/+4
2019-03-13libplist, libusbmuxd: Fix pkgconfig dependency (#10876)Michael Kuhn2-2/+2
pkgconfig is the correct virtual provider.
2019-03-13cubelib, cubew: Add missing pkgconfig dependency (#10875)Michael Kuhn2-0/+2
2019-03-13mpich: Add patch to fix node list parsing (#10870)Michael Kuhn1-0/+7
mpich@3.3 introduced a new regex-based function for node list parsing that does not recognize hostnames without a dash properly.
2019-03-13py-biomine: new package (#10868)Eric Martin1-0/+20
2019-03-13help2man: Add version 1.47.8 and perl runtime dependency (#10862)Eric Martin1-1/+2
2019-03-13py-advancedhtmlparser: new package (#10867)Eric Martin2-0/+38
2019-03-12fqtrim: Create new package (#10861)Eric Martin1-0/+25
2019-03-12Fix mysqldb1 (#9978)David Hows2-2/+17
* Update package.py * Add MYSQL Package file * Fixes for linter
2019-03-12New package: py-mysql-connector (#10327)Elizabeth Fischer2-0/+48
* New package: py-mysql-connector * Fixed docstring * 1. Determined that py-setuptools was not needed at all, so removed. 2. Added py-protobuf. Docs seem to imply that only C protobuf library is required; however, the Python setup.py says differently, and some Python code seems to reference protobuf too. I don't know why this worked for me, but it looks like including py-protobuf is the right thing to do. * Applied solution detailed in: https://github.com/mysql/mysql-connector-python/pull/9 Uncommenting this patch will make `error: option --single-version-externally-managed not recognized` reappear. * Clean up / reorder lines * flake8
2019-03-12Do not use `string` module to be compatible with python 3 (#248) (#10667)Tristan Carel1-3/+2
`string.find` is not part of Python 3 anymore.
2019-03-12varscan: set VARSCAN_HOME variable to jar file location (#10744)Eric Martin1-1/+1
2019-03-12py-pytables: Add hdf5 1.10.x support for versions above 3.4.0 (#10746)Eric Martin1-2/+3
2019-03-12Update caliper package (#10750)David Poliakoff1-11/+23
* Updating Caliper package with a shared lib option * Tightened version bounds on Caliper package * Removed testing. Loosened version constraints * Add Caliper 2.0.1, cleanup dependency specs
2019-03-12find_versions_of_archive: expand link search (#10758)Justin Stanley1-1/+2
2019-03-12Fix clearing EnvironmentModifications with python2 (#10791)Nick Forrington2-1/+8
* Fix clearing EnvironmentModifications with python2 * Add EnvironmentModifications::clear unit test Use re-assignment rather than del to clear array * Fix flake issues
2019-03-12"Werror" too strict for recent compilers (#10802)Rob Latham2-0/+72
rapidjson gives warnings with gcc-7.3 and branch fall through
2019-03-12qt: Use more system dependencies and fix build with new gcc versions (#10817)Michael Kuhn3-2/+53
qt currently falls back to bundled versions of sqlite, harfbuzz, pcre, double-conversion and xcb. This adds the appropriate dependencies and configure arguments. A new variant adds multibyte support to pcre and pcre2, which is required by qt. Additionally, newer versions of gcc (starting with @8.3.0) cause build failures. This adds a patch to fix the problem. The changes have been tested with all versions of qt currently available in Spack. 5.2 and 5.3 do not build for reasons that seem to be unrelated to these changes, though.
2019-03-12casacore does not support fftw+mpi . (#10839)健美猞猁1-1/+1
2019-03-12Aoflagger: a new package. (#10840)健美猞猁1-0/+23
* A new package: aoflagger. * aoflagger does not support boost>1.66.0 . * Add fftw~mpi dependency. * flake8. * Flake8. * Update package heder. * md5 -> sha256.
2019-03-12openPMD-api: shared variant (#10847)Axel Huebl1-0/+4
Add a variant to control shared/static builds (one at a time) and make shared the default.
2019-03-12Revert to manual flag enabling, due to RegCM bug in configure. (#10863)Alberto Chiusole1-2/+5
The configure of RegCM treats --disable-FEATURE as --enable-FEATURE, so we cannot use enable_or_disable.
2019-03-12added checksum for 20190222 release of gnu parallel (#10865)Owen Solberg1-0/+1
2019-03-12py-llvmlite: Add versions 0.26.0 and 0.27.1 (#10866)Eric Martin1-1/+4
2019-03-12New package: ibm-java (#10777)Mark W. Krentel4-1/+75
* Add binary package of the IBM Java SDK for big and little-endian powerpc (power7, 8 and 9). The jdk and openjdk packages only install on x86_64. * Add ibm-java as a java provider * The jdk and openjdk packages only install on x86_64. Add conflicts for ppc64 and ppc64le to jdk and openjdk.
2019-03-12Elfutils package: add m4 dependency and version 0.176 (#10834)wspear1-1/+3
* Elfutils requires m4 to build * Add version 0.176
2019-03-11New package: Draco (#10844)Robert Pavel1-0/+36
2019-03-11scons package: add missing dependency to py-setuptools (#10856)Matthias Diener1-0/+7
2019-03-11OpenMPI: v4.0.0 + Slurm installation error (#10853)Jiawei Zhuang1-4/+11
shmemrun and oshrun do not exist in OpenMPI v4.0.0 (ref: https://www.open-mpi.org/doc/v4.0/) The Spack OpenMPI package was failing the install by trying to remove them. This guards the removal of several scripts when using the Slurm scheduler to handle the case where they don't exist.
2019-03-11Fix URLs for VI-HPS projects (#10821)Michael Kuhn3-3/+3
URLs for the opari2, otf2, and scorep packages have changed (although the checksums are the same)
2019-03-11mpich: add psm2 fabric support (#10814)Stas Sergienko1-2/+10
psm2 is only supported for versions 2.2 and up, so a conflict is added for earlier versions
2019-03-11New package: cotter (#10838)健美猞猁1-0/+20
2019-03-11STAR: Add versions 2.7.0d and 2.7.0e (#10831)Eric Martin1-0/+2
2019-03-11py-chardet: Add version 3.0.2 (#10827)Eric Martin1-0/+1
2019-03-11py-urllib3: Add version 1.21.1 (#10826)Eric Martin1-0/+1
2019-03-11cgns package: add version 3.4.0 and update hdf5 dependency (#10803)Greg Sjaardema1-8/+9
* Add version 3.4.0 * Update checksums for older versions to sha256 * Require hdf5~mpi when building with ~mpi
2019-03-11samtools package: Add version 1.5 and htslib 1.5 dependency (#10825)Eric Martin2-0/+3
2019-03-11hdf5 package: add version 1.10.5 (#10794)Alberto Chiusole1-1/+4
2019-03-11py-crossmap: new package at 0.3.3 (#10854)Justin Stanley1-0/+28
2019-03-11flex: Apply 2.6.4 patch regardless of gcc version (#10841)Michael Kuhn1-10/+8
It seems that this is actually a glibc problem and while 2.6.4 builds without the patch on newer versions of gcc (@8:), it still sometimes segfaults (as observed during the doxygen build).
2019-03-11mpich: remove libpciaccess dependency for MacOS (#10795)Ce Qin1-1/+4
2019-03-11format change and typo in doc (#10848)Shahzeb Siddiqui1-2/+2
2019-03-11Improved detection of Clang versions (#10316)Massimiliano Culpo2-12/+47
Fixes #10191 * Add more regular expressions to detect clang versions that were not being picked up * Add a test for parsing versions from the output of Clang (this does not run Clang, but rather uses example outputs from Clang) * Separate Clang version parsing into its own method (to make it easier to test)
2019-03-11added intel 19.0.3 packages (#10835)Gregory Lee2-0/+4
* added intel 19.0.3 packages * added intel 19.0.3 packages
2019-03-11Add 2019.{3,4} and patches for pedantic warnings. (#10836)Chris Green3-2/+64
2019-03-11boost: patch for problem with warnings for 1.69.0. (#10820)Chris Green3-0/+176
2019-03-08Fix find_headers to also look for C++ headers and Fortran modules (#10798)Michael Kuhn1-3/+6
Currently, only C headers are considered, causing build failures for packages depending on, e.g., netcdf-fortran and xerces-c. Additionally, the regex used to look for the include path component did not consider word boundaries, causing false matches.
2019-03-08breseq package: Add version 0.33.2 and zlib dependency (#10747)Eric Martin1-2/+10
For zlib, also update the `CFLAGS`/`LDFLAGS`
2019-03-08intel: add 2019.3 (#10843)Denis Davydov4-0/+8
2019-03-07Create option to build compilers as needed (#10761)Greg Becker7-65/+137
* Create option to build missing compilers and add them to config before installing packages that use them * Clean up kwarg passing for do_install, put compiler bootstrapping in separate method
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