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2019-10-01picard: add 2.20.8codeandkey1-0/+1
2019-10-01go-md2man: disable module-mode (#12985)Daryl W. Grunau1-0/+1
* go-md2man: disable module-mode * Update var/spack/repos/builtin/packages/go-md2man/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01add singularity 3.4.1 (#12995)Eduardo Arango1-1/+3
* add singularity 3.4.1 Signed-off-by: ArangoGutierrez <eduardo@sylabs.io> * revert some changes Signed-off-by: ArangoGutierrez <eduardo@sylabs.io> * add maintainers list to pkg singularity Add @alalazo and me to the Singularity maintainers list * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01Dataspaces: Fix Fetch URL, Savanna Spec (#13001)Axel Huebl2-2/+2
2019-10-01GCC package: don't set CC etc. based on bin dir if it doesn't exist (#13000)Peter Scheibel1-0/+4
7bcb306 updated setup_environment in the GCC package to examine the bin/ directory to find alternatively-named instances of CC, but this failed to account for when GCC was being installed and failed when it attempted to list the not-yet-existing installation prefix. This commit updates the logic to skip this search if the bin/ directory doesn't exist.
2019-10-01libaio: fixed a condition that checks whether we are running on OS X (#12976)Massimiliano Culpo4-37/+52
* libaio: fixed a condition that checks whether we are running on OS X * libaio: simplified package by adding an explicit conflict for darwin * libaio: added information to the docstring * fio: added version 3.16, added conflict when using libaio, docstring * lvm2: conflict due to libaio dep, improved docstring, simpler install * mariadb: conflict due to libaio dep, improved docstring, version 10.4.7 * mariadb: the dependency on libaio is now conditional, removed conflict * mariadb: fixed a typo in previous commit Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * libaio: turned into a MakefilePackage
2019-10-01Kaldi package: add version 7637de7 and egs (#12911)Jimmy Tang1-0/+8
2019-10-01add new mercurial versions (#12997)Jeffrey Salmond1-1/+3
2019-10-01Update chapel to current (1.19 -> 1.20) (#12991)Christopher Edsall1-1/+2
2019-10-01ADIOS2: 2.5.0 (#12987)Axel Huebl1-0/+1
Add the latest ADIOS2 release, v2.5.0 .
2019-10-01hypre: add version 2.18.0 (#12992)Satish Balay1-0/+1
2019-10-01add adios2 dependency and configuration for newest OpenFOAM (#12993)Mark Olesen1-4/+11
2019-10-01libcerf:add CFLAGS for fujitsu compiler (#12990)noguchi-k1-0/+3
* libcerf:add CFLAGS for fujitsu compiler * fix for flake8
2019-09-30Update nano (#12980)egreen771-3/+51
2019-09-30Revert "update neovim (#12965)" (#12978)Adam J. Stewart1-2/+1
This reverts commit 86a85b7eb22ccf69489a4bfbd947da7dfedcf233.
2019-09-30petsc, slepc: add new versions - 3.12.0 (#12979)Satish Balay2-2/+8
2019-09-30Fix GCC environment variables for external installations (#12454)Seth R. Johnson1-5/+25
Unlike the compiler binary name search logic, the `setup_environment` in GCC's package assumes the compiler names are *exactly* `gcc`, `g++`, etc. In many external installations (Homebrew, Macports) the installation includes only *suffixed* versions such as `gcc-9`. This patch uses the GCC compiler search suffixes to actually locate the correct filenames for the installed compilers, allowing the Spack-generated module file to have useful definitions of CC, CXX, etc. It also allows for the possibility that the user's external installation of GCC is compiled without Fortran support, in which case the `FC` environment variables are not defined.
2019-09-30otf2: add configure args to specify compiler commands. (#12711)t-karatsu1-0/+4
* otf2: add configure args to specify compiler commands. * Modify the reference of the compile commands.
2019-09-29The perl-uri-escape package duplicates perl-uri (#12971)Glenn Johnson6-25/+6
* The perl-uri-escape package duplicates perl-uri The Perl URI::Escape module is in the Perl URI package so the Spack perl-uri-escape package is a duplicate of the perl-uri package. This PR does the following: - replace `depends_on('perl-uri-escape')` with `depends_on('perl-uri')` in packages that dependend on perl-uri-escape - add the version from perl-uri-escape to perl-uri - remove the unneeded dependency from perl-uri - remove the perl-uri-escape package * Reinstated perl-test-needs dependency Put the perl-test-needs dependency for perl-uri back in but set it to type='test'. * For tests to succeed the type must be ('build', 'test')
2019-09-28raxml: simplified recipe by removing SIMD variants (#12952)Massimiliano Culpo1-46/+12
Now the support for SSE3 or AVX is tested on the selected target
2019-09-28bowtie: fix for aarch64, and bugfix about c++11-narrowing. (#12953)t-karatsu3-0/+86
2019-09-28vdt: simplified recipe by removing SIMD variants (#12954)Massimiliano Culpo1-55/+8
Now the support for SSE3 or AVX is tested on the selected target
2019-09-28correct with-xxx-lib= options (#12964)Jaroslav Hron1-1/+1
2019-09-28update neovim (#12965)Patrick Schratz1-1/+2
2019-09-28bolt: add a new version, 1.0rc2 (#12966)Shintaro Iwasaki1-0/+1
2019-09-27eospac: laws.lanl.gov -> laws-green.lanl.gov (#12970)Daryl W. Grunau1-8/+8
2019-09-27py-adios package: restrict python dependency to <=3.6.x (#12932)Ross Miller1-0/+8
The adios code (currently) won't compile against the Python 3.7 C API. This change adds a dependency on 3.6 or less.
2019-09-27Tau package: turn off unsupported variants by default on OSX (#12890)Kevin Huck1-5/+11
2019-09-27New package: libibumad (#12886)G-Ragghianti1-0/+27
2019-09-27New package: maker and dependencies (#12904)Glenn Johnson42-6/+997
2019-09-26qt4: fix 'arch' string due to microarchitecture change (#12957)Seth R. Johnson1-1/+1
qt4 fails to build because it's expecting something like 'x86_64' rather than 'broadwell'.
2019-09-26Update target comparison semantic for a few packages (#12947)Massimiliano Culpo6-14/+14
Use spec.target.family instead of spec.architecture.target
2019-09-26Removed references to '(-march|-mtune|-mcpu)=native' (#12948)Massimiliano Culpo11-37/+10
Now that Spack injects microarchitecture specific optimizations for the selected target, packages should avoid adding flags that could step over those.
2019-09-26parsimonator: simplified recipe by removing SIMD variants (#12949)Massimiliano Culpo1-49/+11
Now the support for SSE3 or AVX is tested on the selected target
2019-09-25New package: flibcpp (Fortran bindings to C++ standard library) (#12926)Seth R. Johnson1-0/+44
2019-09-25butterflypack package: add version 1.0.3 (#12927)liuyangzhuan1-1/+2
2019-09-25interproscan package: add version 4.8, patch for version 5 (#12897)Glenn Johnson3-3/+222
This PR adds interproscan-4.8, which has a completely different build system than version 5. Note that this builds for running on a host as opposed to a queue system. I am fairly certain that a queue system can be configured later. This PR also adds a patch for intrproscan-5 to build when the user building the packages has a large GID by setting posix mode for tar.
2019-09-25libspatialite package: add version 3.0.1 and missing dependencies (#12843)Sinan1-3/+7
2019-09-25py-imageio package: add versions 2.4.1 and 2.5.0 (#12884)Sinan1-0/+2
2019-09-25llvm, mesa: update target comparison semantics (#12914)Matthieu Dorier2-7/+10
* llvm: fixed issues with syntax and formatting * use spec.architecture.target.family * use spec.target instead of spec.architecture.target * mesa: use == instead of __contains__
2019-09-25libflame: fix macOS build (#12950)Adam J. Stewart2-0/+241
2019-09-25openblas: fixed a query to target family (#12910)Matthieu Dorier1-1/+1
2019-09-25portage: fix RelWithDebInfo build (#12944)Christoph Junghans2-0/+19
2019-09-25kokkos-kernels: initial commit (#12934)Christoph Junghans2-0/+106
2019-09-24Upcxx package: remove warning, add version 2019.9.0 (#12880)Mathias Jacquelin1-38/+28
A function added to this package ran as part of importing it and printed a warning for most Spack invocations, this removes the warning message. Also: * Use compilers directly instead of Spack compiler wrappers (since references to the compiler are embedded in text and binary files of the installation) * Add 'cross' variant for setting CROSS environment variable for build * Set UPCXX_INSTALL for generated module files * Set UPCXX_GASNET_CONDUIT/UPCXX_NETWORK in generated module files on Cray systems * Also set UPCXX_NETWORK in build environment for Cray systems
2019-09-24heaptrack: added new package at version 1.1.0 (#12844)Simo Tuomisto1-0/+36
2019-09-24Add missing dependency to perl-xml-parser (#12903)Glenn Johnson1-0/+1
This PR adds the following dependency: + depends_on('perl-libwww-perl', type=('build', 'run'))
2019-09-24Added missing dependencies for perl-list-moreutils (#12900)Glenn Johnson1-0/+3
The following dependencies were added: + depends_on('perl-exporter-tiny', type=('build', 'run')) + depends_on('perl-list-moreutils-xs', type=('build', 'run'))
2019-09-24Added depencies to perl-libwww-perl (#12899)Glenn Johnson1-0/+14
The following dependencies are needed for perl-libwww-perl according to https://metacpan.org: + depends_on('perl-encode-locale', type=('build', 'run')) + depends_on('perl-file-listing', type=('build', 'run')) + depends_on('perl-html-parser', type=('build', 'run')) + depends_on('perl-http-cookies', type=('build', 'run')) + depends_on('perl-http-daemon', type=('build', 'run')) + depends_on('perl-http-date', type=('build', 'run')) + depends_on('perl-http-message', type=('build', 'run')) + depends_on('perl-http-negotiate', type=('build', 'run')) + depends_on('perl-lwp-mediatypes', type=('build', 'run')) + depends_on('perl-net-http', type=('build', 'run')) + depends_on('perl-try-tiny', type=('build', 'run')) + depends_on('perl-uri', type=('build', 'run')) + depends_on('perl-www-robotrules', type=('build', 'run'))
2019-09-24Add missing dependencies to perl-http-daemon (#12898)Glenn Johnson1-0/+2
Added the following dependencies: + depends_on('perl-http-date', type=('build', 'run')) + depends_on('perl-module-build-tiny', type='build')
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