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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
2019-03-07snap: overwrite flags (#10832)Christoph Junghans1-0/+1
2019-03-07cloverleaf3d: overwrite flags (#10830)Christoph Junghans1-0/+10
2019-03-07cloverleaf: overwrite flags (#10829)Christoph Junghans1-0/+10
2019-03-07autofact: fix dependency (#10818)Levi Baber1-1/+1
2019-03-07trimmomatic package: restrict java dependency to version 8 (#10741)Eric Martin1-1/+1
2019-03-07Nix package: update dependencies (#10646)Tristan Carel5-11/+56
* Add 'fiber' as a default library for boost * Add autoconf/automake etc. dependencies to libseccomp package * New package: brotli * New package: editline * Add brotli, editline, boost dependencies to Nix
2019-03-07GEOPM package: add version 1.0.0-rc2 (#10737)Matthias Maiterth1-0/+2
2019-03-07py-sip package: Add version 4.19.3 (#10742)Eric Martin1-1/+2
2019-03-07seqtk package: Add version 1.3 (#10743)Eric Martin1-0/+1
2019-03-07flex package: patch for building 2.6.4 with gcc 7 (#10754)Michael Kuhn1-7/+14
Remove 2.6.3 as preferred version (but keep it available for building). The latest version (currently 2.6.4) is now preferred (according to Spack's defaults).
2019-03-07py-certifi: Add version 2017.4.17 (#10828)Eric Martin1-0/+1
2019-03-07py-flake8: Add missing dependencies for @3.7.7 (#10796)Michael Kuhn3-1/+14
* Update dependencies for py-flake8 when building version 3.7.7 * Add FIXME comment for an example dependency constraint which causes concretization to hang * Add py-entrypoints version 0.3 * Add py-pycodestyle version 2.5.0
2019-03-07CMake package: update libuv dependency constraints (#10824)健美猞猁2-2/+4
* Add libuv version 1.10.0 * CMake versions before 3.12.0 do not build with libuv version 1.25.0, so a constraint is added to build earlier versions of CMake with libuv version 1.10.x
2019-03-07thrust: add versions 1.9.0-1.9.4 (#10823)prs513rosewood1-1/+6
2019-03-06 transdecoder package: Add version 5.5.0 and fix up url and installation ↵Eric Martin1-4/+6
paths (#10745) * Add version 5.5.0 and fix installation locations * URL format has changed as of version 5.5.0 * Update paths created for installation
2019-03-06bsseeker2 package: Add versions 2.1.8 and 2.1.5 (#10748)Eric Martin1-2/+6
As of version 2.1.8, the url format changed, so also update that
2019-03-06Eigen package: support Spack-external builds using Eigen (#10751)Jeongseok Lee1-0/+4
Update CPATH in setup_environment for Eigen, so that the Spack-generated module for Eigen will help builds outside of Spack use the appropriate include prefix for Eigen headers (<install_prefix>/include/eigen3/ rather than <install_prefix>/include/) Note that this only updates the run-time environment, rather than the build-time environment, so Spack builds depending on Eigen that use pkgconfig will not be confused by the presence of the Eigen include directory in CPATH.
2019-03-06scons: add version 3.0.4, cleanup URLs (#10806)Matthias Diener1-6/+4
2019-03-06vtk-m package: turn off mpi support by default (#10755)HAOCHENG LIU1-1/+1
2019-03-06New package: dysco (#10767)健美猞猁1-0/+19
2019-03-06NetCDF package: update constraints on hdf5 mpi support (#10788)Greg Sjaardema1-1/+2
Update NetCDF to require building hdf5 without mpi when NetCDF itself is built without mpi support.
2019-03-06omega-h: add version 9.22.2 and update gcc 8 conflict (#10776)Satish Balay1-1/+2
* Versions before 9.22.2 compiler with gcc 8.3 or later * Added version 9.22.2, which compiles with all gcc 8.x versions (including those before 8.3)
2019-03-06Make is a required dependency of Spack (#10386)Adam J. Stewart1-4/+5
Update documentation on getting started to mention that a "make" executable is required to build packages with Spack.
2019-03-06Update kim-api package and add openkim-models-v2 (#10780)Ryan S. Elliott3-27/+65
* Replace kim-api package with kim-api-v2, which has different versions and removes the 'cmake_args' method * Add openkim-models-v2 as an extension package
2019-03-06libelf: move url to fossies.org (#10815)Mark W. Krentel1-4/+10
* libelf: move url to fossies.org Libelf is no longer maintained and the original mr511.de web site no longer exists. The final release, 0.8.13 from Nov 2009 is still archived at fossies.org. Fixes #10757. * Change the homepage to the FSF entry.
2019-03-06added python 2.7.16 (#10805)Gregory Lee1-1/+2
2019-03-06build fixes for util-linux (#10811)Gregory Lee1-7/+2
2019-03-06unifycr: dependency changes and new version (#10722)Cameron Stanavige1-25/+13
New release of UnifyCR. Remove unsupported pre-1.0 versions UnifyCR has had a few dependency changes to make the backend more efficient. A new pre-release version has been released as well to mark these changes. Prior versions are no longer supported.
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