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2020-03-16Warn only if link target is not relative and outside of the install prefix ↵Patrick Gartung1-9/+8
(#15512)
2020-03-16veccore: added package at v0.6.0 (#15472)Seth R. Johnson1-0/+40
2020-03-16When replacing path text in ELF binaries do not include null byte padding in ↵Patrick Gartung1-1/+1
search string (#15508)
2020-03-16CMakePackage: convert variants to CMake arguments (#14376)Seth R. Johnson4-16/+161
Add a 'define_from_variant` helper function to CMake-based Spack packages to convert package variants into CMake arguments. For example: args.append('-DFOO=%s' % ('ON' if '+foo' in self.spec else 'OFF')) can be replaced with: args.append(self.define_from_variant('foo')) The following conversions are handled automatically: * Flag variants will be converted to CMake booleans * Multivalued variants will be converted to semicolon-separated strings * Other variant values are converted to CMake string arguments This also adds a 'define' helper method to convert any variable to a CMake argument. It has the same conversion rules as 'define_from_variant' (but operates directly on values rather than requiring the user to supply the name of a package variant).
2020-03-16silo: depends on hdf5@:1.10.999 (#15495)Erik Schnetter1-0/+1
Silo does not build with HDF5 1.12.
2020-03-16Buildcache: Install into non-default directory layouts (#13797)Patrick Gartung4-585/+896
* Buildcache: Install into non-default directory layouts Store a dictionary mapping of original dependency prefixes to dependency hashes Use the loaded spec to grab the new dependency prefixes in the new directory layout. Map the original dependency prefixes to the new dependency prefixes using the dependency hashes. Use the dependency prefixes map to replace original rpaths with new rpaths preserving the order. For mach-o binaries, use the dependency prefixes map to replace the dependency library entires for libraries and executables and the replace the library id for libraries. On Linux, patchelf is used to replace the rpaths of elf binaries. On macOS, install_name_tool is used to replace the rpaths and dependency libraries of mach-o binaries and the id of mach-o libraries. On Linux, macholib is used to replace the dependency libraries of mach-o binaries and the id of mach-o libraries. Binary text with padding replacement is attempted for all binaries for the following paths: spack layout root spack prefix sbang script location dependency prefixes package prefix Text replacement is attempted for all text files using the paths above. Symbolic links to the absolute path of the package install prefix are replaced, all others produce warnings.
2020-03-16tixi: added package at v3.0.3 (#15490)Melven Roehrig-Zoellner1-0/+24
2020-03-16swig: added v4.0.1 (#15496)Erik Schnetter1-0/+1
2020-03-16ncurses: added v6.2 (#15494)Erik Schnetter1-0/+1
2020-03-16cmake: added v3.16.5 (#15492)Erik Schnetter1-0/+1
2020-03-16unqlite: added package at v1.1.9 (#15501)Matthieu Dorier1-0/+18
2020-03-15gcc: Don't apply macOS 9.2.0 patch for 9.3.0 (#15493)Erik Schnetter1-1/+1
The patch neither applies nor is necessary.
2020-03-14Limit binutils to <= 2.33.1 (#15470)Tim Haines1-1/+1
HPCToolKit <= 2020.03.01 does not build with binutils 2.34.
2020-03-13LIBXSMM 1.15 (#15482)Hans Pabst1-2/+3
* LIBXSMM 1.15 * LIBXSMM: renamed development version according to the related branch on GitHub.
2020-03-13py-astpretty: add new package (#15484)Adam J. Stewart1-0/+21
* py-astpretty: add new package * pkg_resources needed at run-time
2020-03-13package: Add fetch_options variable (#15317)Michael Kuhn14-42/+122
PR #15212 added a new connect_timeout option that can be overridden using fetch_options but had to specified per-version. This adds a new per-package variable that can be used to override fetch_options for all versions in the package. This includes connect_timeout as well as 'cookie' (e.g. for the jdk package). Packages can combine package-level fetch_options with per-version fetch_options, in which case the version fetch_options completely override the package-level fetch_options. This commit includes tests for the added behavior.
2020-03-13pgi: add missing paths in setup_run_environment (#15480)Melven Roehrig-Zoellner1-0/+3
2020-03-13Add py-h5glance versions 0.5 & 0.6 (#15461)Thomas Kluyver1-1/+3
* Add py-h5glance versions 0.5 & 0.6 * List versions newest to oldest
2020-03-13Add new ACTS version (#15479)Hadrien G1-0/+1
2020-03-13gitignore: pytest cache directory (#15476)Adam J. Stewart1-0/+1
2020-03-12Add source highlight package (#15473)Hector1-0/+21
* add GNU source-highlight package * fix flake8 * Allows the package to download from GNU mirrors
2020-03-12gcc: Add 9.3.0 (#15469)Michael Kuhn1-0/+1
2020-03-12cpprestsdk: fix common error and, use boost@1.69.0 or lower (#15463)noguchi-k2-1/+51
2020-03-12testing: increase installer coverage (#15237)Tamara Dahlgren3-109/+280
2020-03-12Add Caliper v2.3.0 (#15468)David Böhme1-1/+2
2020-03-12Add package jblob-3.0 (#15400)Amjad Kotobi1-0/+35
2020-03-12Change py-merlinwf to py-merlin (#15453)Joe Koning5-103/+25
* Change py-merlinwf to py-merlin to match PyPi. Change py-merlin to py-merlin-info. Move to py-merlin_info. Add py-merlin-info back in. * Update dependent packages for the new merlin name. * Remove non-working pyre and the associated packages, exchanger, py-pythia and py-mlerin-info from citcoms. * Remove blank line.
2020-03-12pfunit: add max_array_rank=(int) variant (#15348)Bryce Allen1-2/+7
* pfunit: add max_array_rank=(int) variant * pfunit: flake8 line length fixes
2020-03-12Update plumed 2.5.4 and 2.6.0 (#15462)Zhiyi Wu1-2/+3
Co-authored-by: zhiyiwu <zhiyi.wu@gtc.ox.ac.uk>
2020-03-12likwid: add compiler selection for ARM and POWER architecture (#14183)Thomas Gruber1-4/+7
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-03-12plumed: add cython as dependency (#15460)Jeffrey Salmond1-0/+1
2020-03-12Creating versions from urls doesn't modify class attributes (#15452)Massimiliano Culpo3-3/+3
fixes #15449 Before this PR a call to pkg.url_for_version was modifying class attributes determining different results for subsequents calls and an error when the urls was empty.
2020-03-12Minor updates to CI configuration (#15458)Massimiliano Culpo2-1/+2
* Check on Python versions uses action/checkout@v2 * Update the apt cache before installing system packages
2020-03-11add new package: lmbench (#15457)darmac1-0/+30
* add new package: lmbench * refine LDFLAGS append call
2020-03-11revbayes: Update URLs and hashes for old archives (#15451)Nick Booher1-4/+10
* revbayes: Update URLs and hashes for old archives * Switch to url_for_version * Fix whitespace
2020-03-11Update package.py for HDF5 1.12.0 release (#15430)Les Kurz1-0/+2
* Update package.py * Update package.py * add upper bounds to production config_option * fix config_options * Fix mistaken changes.
2020-03-11add new package: php (#15435)darmac1-0/+41
2020-03-11cpio: icc -no-gcc (#15446)Daryl W. Grunau1-0/+5
Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2020-03-11binutils: Add missing texinfo dependency (#15444)Michael Kuhn1-0/+4
2020-03-11add new package: keyutils (#15433)darmac1-0/+27
2020-03-11add hatchet python package (#15428)Stephanie Brink1-0/+27
2020-03-11libfabric@1.9.1: Add fabtests (#15440)Dr. Christian Tacke1-0/+4
The test utils for the new version 1.9.1 are missing. Add them.
2020-03-11Package for the resultsFile Python module (#15088)Anthony Scemama1-0/+22
* Added resultsFile package * Added comments * Fixed PEP8 * Added Python3 package * Removed py-setuptools
2020-03-11Horovod (#15380)rvinaybharadwaj2-0/+88
2020-03-11bugfix: resolve undefined source_pkg_dir failure (#15339)Tamara Dahlgren2-8/+74
2020-03-11fetch_strategy: remove vestigial code (#15431)Greg Becker1-18/+0
2020-03-11kealib: moved to github, added v1.4.12 (#15436)Neil Flood1-3/+4
2020-03-10Add valgrind variant to petsc (#15427)Hector1-1/+4
* Add PETSc valgrind dependency * Remove +debug on valgrind dependency * enh variant description
2020-03-10Fix OpenBLAS 0.2 build, 0.38+ Intel builds, and variant name (#15419)Seth R. Johnson2-19/+44
* Remove ARCH argument in OpenBLAS < 0.3.0 * Fix Intel OpenBLAS that uses lapack 0.3.9 * Improve variant name consistency see https://github.com/spack/spack/issues/15239
2020-03-10gcc: backporting fix for glibc 2.31 (#15403)Mathias Anselmann3-0/+114
* backporting fix for building gcc >= 8.1.0 and gcc <= 9.2.0 with binutils 2.31 * removed trailing whitespace
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