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2018-08-11r-goplot: new package (#8942)Levi Baber1-0/+49
2018-08-11r-findpython: new package (#8943)Levi Baber1-0/+37
2018-08-11r-sm: new package (#8945)Levi Baber1-0/+39
2018-08-11Add version 5.1.5 for gromacs. (#8948)健美猞猁1-0/+1
2018-08-11Add version 1.12.8 to dbus (#8949)Tom Merrick1-0/+1
2018-08-11r-bindrcpp: add new version (#8950)Levi Baber1-1/+1
* r-bindrcpp: add new version * r-bindrcpp: version ordering and removing r version restriction
2018-08-11Add new versions for cmake. (#8955)健美猞猁1-0/+3
2018-08-11Gromacs conflicts with cmake@3.10: . (#8956)健美猞猁1-2/+2
2018-08-10r-biasedurn: new package (#8937)Levi Baber1-0/+40
* r-biasedurn: new package * r-biasedurn: add list_url
2018-08-10r-amap: new package (#8935)Levi Baber1-0/+38
* r-amap: new package * r-amap: add list_url * r-amap: dep type
2018-08-10r-fastcluster: new package (#8934)Levi Baber1-0/+46
* r-fastcluster: new package * r-fastcluster: add list_url
2018-08-10Phist 1.6.1 (#8933)jthies1-0/+3
* packages/phist: new version 1.6.1 * packages/phist: depends on Python 3.x for generating Fortran and C++ bindings * packages/phist: new version 1.7.2 * phist: depend on python@3 only for versions later than 1.7 * packages/phist: depend on python@3: rather than 3 * phist: python dependency is type='build', thans @adamjstewart
2018-08-10Branch with the meson build-system (#8467)Tom Merrick9-0/+309
* Branch with the meson build-system * Fix build_environment for dual loads and add create code * Add documentation * Fixed option list * Update build_system_guess for meson * Fixed documentation errors * Added meson to build and configure and updated documentation * fix typos
2018-08-09boost: add 1.68.0 (#8931)Denis Davydov1-0/+1
2018-08-09spec: make full_hash look like dag_hash (#8911)Scott Wittenburg1-2/+7
2018-08-09add fgfs variant to stat and develop version (#8919)Gregory Lee3-3/+95
2018-08-09perl6-slurp: new package (#8672)Levi Baber1-0/+36
* perl6-slurp: new package * perl-perl6-slurp: changing perl version dependency
2018-08-09Remove duplicate variant in Boost package (#8923)Hadrien G1-2/+0
2018-08-09bugfix: cc handles spaces in flag variables properlyTodd Gamblin2-90/+82
- cc cleanup caused a parsing regression in flag handling - We added proper quoting to array expansions, but flag variables were never actually converted to arrays. Old code relied on this. This commit: - Adds reads to convert flags to arrays. - Makes the cc test check for improper space handling to prevent future regressions.
2018-08-09libiberty: new package (#8912)Mark W. Krentel1-0/+73
* libiberty: new package The libiberty.a library from GNU binutils. Libiberty provides demangling and support functions for the GNU toolchain. This package uses the binutils tarfile but only builds the libiberty subdirectory. This is useful for other packages that want the demangling functions without the rest of binutils. Add variant 'fpic' to compile with -fPIC. Addresses some issues raised in PR #8806. * libiberty: change variant name to 'pic'. Allow libiberty to install the library in lib64 and don't try to copy it to lib.
2018-08-08ECP VELOC Package update (#8910)Elsa Gonsiorowski, PhD7-9/+12
* update of veloc & dep versions (replace old non-working versions) * veloc doesn't work with gcc <= 4.9.3 * explicitly pass MPI to CMake for veloc build
2018-08-08superlu_dist should be built with 'HAVE_PARMETIS=TRUE'. (#8917)Satish Balay1-0/+1
2018-08-08cc: refactor flag adding so that it's not in reverse orderTodd Gamblin2-29/+56
- flags were prepended in reverse order to args, but this makes it hard to see what order they'll be in on the final command line. - add them in the order they'll appear to make cc easier to maintain. - simplify code for assembling the command line - fix separator used in SPACK_SYSTEM_DIRS test
2018-08-08cc: restore ccache support in the wrapper, add a regression testTodd Gamblin2-2/+38
- Add back ccache support to the wrapper. - Add a regression test to make sure ccache is working properly.
2018-08-08cc: run shellcheck linter on the cc compiler script, minor cleanupTodd Gamblin2-12/+14
- This corrects most of the issues found by shellcheck - This also uses ':' as the delimiter for SPACK_SYSTEM_DIRS, for consistency with other variables.
2018-08-08cc: don't use sed to filter system directoriesTodd Gamblin2-42/+93
- filtering using sed causes most builds to slow down quite a bit, as the compiler wrapper has to run sed many times, and *it* runs many times - do the system directory parsing directly in bash
2018-08-08refactor: clean up and fix the cc testTodd Gamblin2-414/+503
- Add tests to ensure that RPATHs are not added in cc mode, which can cause some builds to fail. - Change cc.py to use pytest style - Instead of writing out all the flags, break the flags down into variables so that it's easy to read what each test is supposed to check. This should make cc.py more maintainable in the future.
2018-08-08bugfix: cc should not add -L or -Wl,-rpath in compile-only modeTodd Gamblin1-80/+108
- Adding -L and -Wl,-rpath to compile-only command lines ("cc mode" or "-c") causes clang (if not also other compilers) to emit warnings that confuse configure systems. - Clang will print warnings about unused command-line arguments. - This fix ensures that -L and -Wl,-rpath are not added if the compile line is just building an object file with -c - This also cleans up the cc script in several places.
2018-08-08Restore cc: package search paths come before dependency paths (#4692)Gregory Becker4-158/+330
Spack currently prepends include paths, library paths, and rpaths to the compile line. This causes problems when a header or library in the package has the same name as one exported by one of its dependencies. The *dependency's* header will be preferred over the package's, which is not what most builds expect. This also breaks some of our production codes. This restores the original cc behavior (from *very* early Spack) of parsing compiler arguments out by type (`-L`, `-I`, `-Wl,-rpath`) and reconstituting the full command at the end. `<includes> <other_args> <library dirs> <rpaths>` This differs from the original behavior in one significant way, though: it *appends* the library arguments so that dependency libraries do not shadow those in the build. This is safe because semantics aren't affected by *interleaving* `-I`, `-L`, and `-Wl,-rpath` arguments with others, only with each other (so the order of two `-L` args affects the search path, but we search for all libraries on the command line using the same search path). We preserve the following: 1. Any system directory in the paths will be listed last. 2. The root package's include/library/RPATH flags come before flags of the same type for any dependency. 3. Order will be preserved within flags passed by the build (except system paths, which are moved to be last) 4. Flags for dependencies will appear between the root flags and the system flags, and the flags for any dependency will come before those for *its* dependencies (this is for completeness -- we already guarantee this in `build_environment.py`)
2018-08-07elfutils: update version and add variants (#8891)Mark W. Krentel1-8/+40
* elfutils: update version and add variants Add latest version 0.173. Add variants bzip2, xz and zlib to support reading compressed DWARF sections, default True. Move maintainer-mode to a variant with default False. This is only useful for developers who want to modify the source for generated files. * Add dependency on zlib for reading compressed DWARF sections. Add variants to use bzip2 and xz for compressed sections. Remove maintainer mode and the dependencies on flex and bison. These are not used for one-time builds. Be sure to squash both the commits and the commit messages.
2018-08-07Fixing the addition curly brackets to conform to the rest of the templates ↵Micheal Quinn1-1/+1
usage of a literal curly bracket
2018-08-07Adding logic to the autoload if statement so it only fire if the module is ↵Micheal Quinn1-1/+1
being loaded.
2018-08-07Fix performance issue when compiling. (#8828)cedricchevalier191-4/+3
* Fix performance issue when compiling. Spack was doing active wait when compiling, spoiling one core. My fix consists in not setting any timeout for select, instead of the previous 0 second. * Fix comments about select.select timeout
2018-08-07Add libs attribute to mesa and mesa-glu packages (#8904)Adam J. Stewart5-10/+17
Also fix dependency version in glvis package. Fixes build errors mentioned in #8454.
2018-08-06libstdc++ detection uses os.path.realpath instead of os.readlink (#8865)Paul Chelarescu1-1/+1
2018-08-06spack general packages.yaml defaults: add unwindGeoffrey Malcolm Oxberry1-0/+2
This commit adds 'libunwind' as the default 'unwind' provider in spack. This preference should be overridden by the darwin/packages.yaml file on macOS. Continues the changes discussed in
2018-08-06caliper: update to use unwind virtual packageGeoffrey Malcolm Oxberry1-1/+1
2018-08-06gperftools: use unwind virtual packageGeoffrey Malcolm Oxberry1-1/+1
2018-08-06mfem+libunwind: use "unwind" virtual packageGeoffrey Malcolm Oxberry1-2/+2
2018-08-06darwin packages.yaml defaults: add unwind providerGeoffrey Malcolm Oxberry1-0/+7
This commit adds default unwind providers to the default packages.yaml for darwin. Compiler versions are supplied with the apple-unwind package so that apple-unwind is only used with Apple's clang fork, and not with LLVM's clang.
2018-08-06apple-libunwind: new package, provides unwindGeoffrey Malcolm Oxberry1-0/+84
This commit continues the changes discussed in #8823 by creating a new "apple-libunwind" placeholder package that supplies instructions for how to configure packages.yaml to register Apple's libunwind implementation with spack. This package also provides the "unwind" virtual package representing the libunwind base API. The clang-apple compiler version should be specified in packages.yaml so that apple-unwind is only used with Apple's clang compiler, not the stock LLVM compiler.
2018-08-06Make libunwind provider of unwind virtual pkgGeoffrey Malcolm Oxberry1-0/+2
This commit begins addressing the ideas discussed in #8823. The libunwind library now provides the "unwind" virtual package, which represents the "libunwind base API" common to LLVM libunwind, Apple's LLVM libunwind, and non-GNU libunwind.
2018-08-06py-crossmap: needs py-setuptools (#8898)Levi Baber1-1/+3
* py-crossmap: needs py-setuptools * py-crossmap: additional deps * py-crossmap: make bx build/run
2018-08-06add Charliecloud 0.9.1 (#8902)Reid Priedhorsky1-0/+1
2018-08-06Remove default variant bug from list of known issues (#8900)Adam J. Stewart1-32/+0
2018-08-06Docstring typo: builing -> building (#8896)George Hartzell1-1/+1
2018-08-06Bump R to v3.5.1. (#8895)健美猞猁1-0/+1
2018-08-06Libtool: version 'develop' (#8894)Sergey Kosukhin2-0/+34
* libtool: add version 'develop'. * libtool: patch: correct parsing of compiler output when collecting predeps and postdeps.
2018-08-06 modified: var/spack/repos/builtin/packages/py-pytest/package.py (#8890)Sajid Ali1-1/+2
2018-08-06LIKWID: Switch to perf_event backend to allow user installations but with ↵Thomas Roehl1-6/+14
limited features (#8886) * Switch to perf_event backend to allow user installations but with limited features. * Fix flake8 issues * Fix flake8 issues remove filter for INSTALL_CHOWN * Incorporate the comments