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2019-07-18stacks: update view management for multiple/combinatorial viewsGregory Becker2-2/+2
This adds notion of a default view, other views in environments
2019-07-18cmake: add version 3.15.0 (#12058)Matthias Diener1-0/+1
2019-07-18Add master version to sklearn (#12057)Adam J. Stewart1-3/+16
2019-07-18pkg PRRTE: added version 1.0.0 (#12054)Matthieu Dorier1-1/+2
2019-07-18added version 3.1.3 of PMIx (#12055)Matthieu Dorier1-1/+2
2019-07-18Workaround for #9149 (#12050)Adam J. Stewart1-9/+12
2019-07-18py-mlxtend: new package at 0.16.0 (#12039)Justin S1-0/+23
* py-mlxtend: new package at 0.16.0 * py-mlxtend: fix dependencies
2019-07-17update web site and git url for BMI package (#12036)Phil Carns1-2/+2
2019-07-17add charliecloud v0.10 (#12046)Jordan Ogas1-0/+1
2019-07-17Fix scikit-learn build with Apple clang (#11496)Adam J. Stewart4-14/+111
* Fix scikit-learn build with Apple clang * Update compiler unit tests * Fix unit tests * Fix OpenMP dep * recursive=True no longer necessary * Add myself as a maintainer * Specify which versions require OpenMP * Typo fixes * LLVM-OpenMP is the correct dependency, no OMPT * Flake8 fix * Undo Apple Clang OpenMP flag change, split into a separate PR
2019-07-17libjpeg-turbo: set compiler flags with CMake args (#11938)t-karatsu1-0/+18
Later versions of libjpeg-turbo build with CMake; to build with user-specified cflags, the user must supply these to CMake as -DCMAKE_C_FLAGS (Spack's typical approach of injecting these flags into the compiler wrapper invocation is insufficient in this case). Currently libjpeg-turbo cannot be implemented as a CMakePackage (and thereby take advantage of the flag_handler implementation it provides) because not all versions of libjpeg-turbo use CMake, so this adds a custom implementation of flag_handler and flags_to_build_system_args to libjpeg-turbo.
2019-07-17Add support for .txz and .tbz2 file extensions (#12048)Adam J. Stewart2-8/+4
2019-07-17kim-api 2.1.0 (#12041)Ryan S. Elliott1-1/+2
2019-07-17package opencoarrays: add new version: 2.7.1 (#12043)brietzke1-0/+1
2019-07-17Cmake/add option for fujitsu compiler (#11839)t-karatsu1-0/+6
* cmake: change c++ spec when building with Fujitsu compiler. * cmake: define cxxflags using a Fujitsu compiler's method. * cmake: Add condition of whether to add cxx11 option.
2019-07-16Added url_for_version to python/package.py (#12040)Shane R. Spencer1-0/+4
2019-07-16py-pandas: add 0.24.2 (#12038)Justin S1-0/+1
2019-07-16r: set FPICFLAGS for compilers except 'gcc' (#12033)Hironori-Yamaji1-0/+4
2019-07-16package mutationpp: add new version: 1.0.0 (#12035)brietzke1-0/+1
2019-07-15qt: fix patch checksum (#12024)Michael Kuhn1-1/+1
It seems that GitHub's output changed slightly for this patch (one more letter for both short hashes on the index line), probably due to the number of objects in the repository.
2019-07-15binutils: Adding Clang to narrowing conversion error workaround (#12029)Brian Homerding1-1/+2
2019-07-15Add JUBE package definition (#12023)Marc-Andre Hermanns1-0/+41
* Add JUBE package definition * Fixing flake8 errors
2019-07-15Added HPX version 1.3.0. (#12025)Severin Strobl1-0/+1
2019-07-15boost: use clang toolset when building with Fujitsu compiler. (#11827)t-karatsu1-1/+2
2019-07-15Add auto-dispatch specification to Intel packages (#11697)Glenn Johnson2-0/+26
This PR adds the ability to specify the auto-dispatch targets that can be used by the Intel compilers. The `-ax` flag will be written to the respective compiler configuration files. This ability is very handy when wanting to build optimized builds for various architectures. This PR does not set any optimization flags, however.
2019-07-15binutils: added '-Wno-narrowing' to CXXFLAGS when using fj compiler via ↵Hironori-Yamaji1-0/+8
flag_handler (#11922) FJ compiler fails for older versions w/o '-Wno-narrowing' flag.
2019-07-15packages: computation.llnl.gov is now computing.llnl.gov (#12013)Todd Gamblin14-23/+23
2019-07-15py-basemap: install without egg (#11961)Milton Woods1-1/+2
* py-basemap: avoid creating egg during build, for compatibility with mpl_toolkits * py-basemap: not ready for py-pyproj@2 onwards
2019-07-14gdb: add version 8.3 (#12018)Matthias Diener1-0/+1
2019-07-14make cfitsio explicitly depend on curl (#12016)Reinhard Prix1-0/+1
- currently would revert to using system-curl instead, pulling in unwanted system dependencies and lib-paths
2019-07-14bzip2: Add 1.0.8 (#12017)Michael Kuhn1-4/+2
Update URLs to official ones.
2019-07-13Make JDK version more specific (#12008)Adam J. Stewart1-1/+1
2019-07-13Add py-jsonschema 2.6.0 (#12009)Adam J. Stewart1-1/+2
2019-07-12find_libraries searches lib and lib64 before prefix (#11958)Tim Fuller3-24/+10
The default library search for a package checks the lib/ and lib64/ directories for libraries before the root prefix, in order to save time when searching for libraries provided by externals (which e.g. may have '/usr/' as their root). This moves that logic into the "find_libraries" utility method so packages implementing their own custom library search logic can benefit from it. This also updates packages which appear to be replicating this logic exactly, replacing it with a single call to "find_libraries".
2019-07-12New package: Nim (#11649)xfzhao1-0/+41
2019-07-12r package: add rmath variant for standalone rmath library (#11693)Justin S1-0/+14
2019-07-12new package: umap (#12000)egreen771-0/+35
2019-07-12jdk: Add the 'provides' call (#11997)Hironori-Yamaji1-0/+1
2019-07-12Update libensemble (#11990)Stephen Hudson1-1/+2
2019-07-12update scalasca to latest version, simplify recipe (#11999)Phil Tooley1-3/+7
add list_url for use with spack checksum
2019-07-11Modifications to r package (#11957)Glenn Johnson1-7/+21
This PR has several modifications for the r package. - The tk package is always depended on but this pulls in X11, making the 'X' variant non-functional. This PR sets a dependency of tk on '+X'. - There is a missing dependency on libxmu when '+X' is set. - The libraries for R wind up in a non-standard location and are thus left out of the RPATH settings. This PR adds that directory to RPATH. - The MKL integer interface for gfortran is not in the BLAS libs. This PR replaces the intel interface with the gfortran interface if needed. - Use the `LibraryList` `ld_flags` method for blas as that is more in line with th R Installation and Administration manual. Note that this PR depends on PR #11956. This PR closes #8642.
2019-07-11Add variants for tk package (#11956)Glenn Johnson1-3/+16
TK can be built with support for libXft and X Screensaver. Both of these are turned on in the Tk configure script. That means the system libraries will get picked up if they are on the system and nothing is specified in the package. Since the default for both of them is 'True' I set the default value for the variants to 'True'.
2019-07-11bowtie2: Add version 2.5.3.1 and fix to build on ARM (#11974)Toyohisa Kameyama1-1/+14
* bowtie2: Add version 2.5.3.1 and fix to build on ARM 1. Add version 2.5.3.1. 2. Add simde for ARM. 3. Disable -fopenmp-simd when gcc 4.8.X or before for ARM. 4. Add Makefile option POPCNT_CAPABILITY=0 for ARM. * flake8.
2019-07-11velvet: remove -m64 on aarch64. (#11984)Toyohisa Kameyama1-0/+5
2019-07-11Boost: Compile with toolset=clang for Arm compiler (#11992)Nick Forrington1-1/+7
Bootstraps with gcc, but compiles with clang
2019-07-11megahit package: add patch to build on ARM. (#11963)Toyohisa Kameyama2-0/+22
2019-07-11New package: dimemas (#11979)Phil Tooley1-0/+34
2019-07-11OpenFOAM package: update download url (#11973)Mark Olesen1-2/+2
2019-07-11libfabric package: add support for tcp provider (#11965)Phil Carns1-1/+2
2019-07-11luit package: use autotools. (#11962)Toyohisa Kameyama1-8/+4
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