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2017-11-02filesystem_view: do not link external packagesBen Boeckel1-0/+10
2017-11-02filesystem_view: add a class to handle a view via a Yaml descriptionOliver Breitwieser1-0/+524
2017-11-02package: support removing dependencies when deactivatingOliver Breitwieser1-6/+14
2017-11-02conftest: mock out spack.store.extensions as wellBen Boeckel1-0/+4
2017-11-02views: support querying view layouts as wellOliver Breitwieser5-26/+56
This abstracts out the layout in use between the global installations and a specific view.
2017-11-02link_tree: support choosing the link functionOliver Breitwieser1-2/+2
This can be used to make hardlinks rather than symlinks.
2017-11-02link_tree: support ignoring conflictsOliver Breitwieser1-3/+16
2017-11-02directory_layout: add a YamlExtensionsLayout classOliver Breitwieser1-0/+25
This uses a view to query extensions.
2017-11-02link_tree: only remove matching files when unmergingOliver Breitwieser1-1/+6
2017-11-02directory_layout: factor out an ExtensionsLayout classOliver Breitwieser1-92/+118
2017-11-02extensions: add an installed_extensions_for methodBen Boeckel2-1/+11
2017-11-02database: rename `installed_extensions_for`Oliver Breitwieser3-3/+3
Views support activating packages, so rename the method because it will soon query what is activated versus what is installed.
2017-11-02package: support verbosity when activatingOliver Breitwieser1-8/+14
2017-11-02package: rename `activated` to `is_activated`Oliver Breitwieser4-10/+10
This allows the activation code to be later given parameters.
2017-11-02cmd/test: fix a typo in a commentBen Boeckel1-1/+1
2017-11-02spec_yaml: fix a typoBen Boeckel1-1/+1
2017-11-02view: fix a typoOliver Breitwieser1-1/+1
2017-11-02determine full compiler version for gcc-7Ben Boeckel1-1/+4
Fixes #5778. Spack uses 'gcc -dumpversion' to determine the full version of gcc. 'gcc -dumpversion' no longer gives the full version on gcc 7.2.0. 'gcc -dumpfullversion' is required instead. This PR detects when 'gcc -dumpversion' gives a truncated version of '7' and in that case retrieves the full version with 'gcc -dumpfullversion'
2017-11-02bdftopcf: require xproto and fontsproto at build time (#6112)Ben Boeckel1-0/+2
These are technically "link" depends of libxfont, but they have no actual libraries. Fixes #5936.
2017-11-02Add package r-reportingtools and update url for its dependencies. (#6071)lingnanyuan4-5/+71
* r-reportingtools: Create new package. * r-go-db: Update url. * r-gseabase: Update url. * r-pfam-db: Update url.
2017-11-02adios: Fix hdf5 and sz dependencies (#6016)Michael Kuhn1-2/+2
- hdf5's +hl variant is required because the build uses libhdf5_hl. - sz is only compatible up to version 1.4.10 because the library has been renamed to libSZ in 1.4.11.
2017-11-02hwloc: add version 1.11.8 (#6099)Brice Goglin1-0/+1
Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
2017-11-02arlecore: new package (#6109)Audrey Thoma1-0/+40
2017-11-02Only use XCode clang wrappers for packages that set use_xcode=True (#6077)Todd Gamblin3-23/+11
2017-11-02gromacs: add develop version (#6098)Christoph Junghans1-0/+1
2017-11-02sundials+hypre depends on hypre (#6075)Adam J. Stewart1-0/+2
2017-11-02the-silver-searcher: add missing dependency (#6095)Denis Davydov1-0/+1
2017-11-02xqilla: Use append instead of extend (#6094)Michael Kuhn1-1/+1
2017-11-01Update candle (#6097)Brian Van Essen1-0/+10
2017-11-01update filename used for cc wrapper invocation debug log (#5837)scheibelp3-3/+8
The name of the debug log written by the cc compiler wrapper was given by Spec.short_spec, which includes the architecture. Somewhere along the line Spec.format started adding spaces around the architecture property so the filename started including spaces; the cc wrapper script appears to ignore this, so files like spack-cc-bzip2-....in.log (which record the wrapped compiler invocations) were not being generated. This uses a different format string from the spec to generate the wrapper log file names (which does not include spaces).
2017-11-01Fix user specs which include already-installed packages (#5939)scheibelp2-1/+7
* when a user-provided spec refers to an already-installed package, packages with patches applied were causing validation errors based on the recorded variants in the package's class * avoid checks on all reserved variants (not just 'patches')
2017-11-01r-getoptlong: created new package (#6069)Yifan Zhu1-0/+42
2017-11-01r-gtrellis: created new package (#6088)Yifan Zhu1-0/+46
2017-11-01LBANN flags and OpenCV variant (#5951)Brian Van Essen3-13/+39
* Fixed the datatype flag in the LBANN package. Fixed where the datatype flag should be set. * Added variant to OpenCV to disable building DNN support * Fixed a bug in how the elemental package tries to find its Fortran library. The current method does not work with Intel compilers. * Added necessary paths for cuDNN and CUB. * Addressed flake8 issues in Elemental package. * Fixed several flake8 errors. Added variant to build with or without support for arbitrary-precision floating point arithmetic. * Added the proper CMake flag when MPFR support is disabled. * Fixed a bug in how the cudnn path was being set when there was no cudnn requested. Also requested that OpenCV is built without eigen support. * Fixed another bug where a dependency may not be there and thus should not be always checked.
2017-11-01lua: Build a shared library (#6008)Michael Kuhn2-0/+77
Patch is inspired by Arch Linux and Homebrew.
2017-11-01r-circlize: new package (#6087)Yifan Zhu1-0/+48
2017-11-01r-alsace: Create new package. (#6064)lingnanyuan1-0/+43
2017-11-01r-globaloptions: new package (#6068)Yifan Zhu1-0/+40
2017-11-01r-affycoretools: Create new package and its dependency r-ff. (#6082)lingnanyuan2-0/+92
* r-ff: Create new package * r-affycoretools: Create new package. * r-ff: update url.
2017-11-01r-agimicrorna: Create new package. (#6083)lingnanyuan1-0/+41
2017-11-01r-complexheatmap: created new package (#6084)Yifan Zhu1-0/+46
2017-11-01r-shape: created new package (#6086)Yifan Zhu1-0/+36
2017-11-01r-pmcmr: new package (#6085)Yifan Zhu1-0/+47
2017-11-01Opencv eigen (#6014)Brian Van Essen1-1/+1
* Added a package for the MDAnalysis toolkit. * Changed dependency for the eigen library to not include support for multiple-precision (arbitrary-precision) floating point arithmetic, since OpenCV does not support these data types. * Fixed incorrect implementation
2017-11-01flux: update flux-core to v0.8.0 (#5914)Mark Grondona3-14/+19
* dockbook: remove update to dependent environment Remove override of setup_dependent_environment in both docbook-xml and docbook-xsl, which seems to generate a warning from spack about "Suspicious requests to set or unset 'XML_CATLOG_FILES' found." * flux: update version/dependencies to 0.8.0 Update flux-core to v0.8.0. Clean up dependencies and remove unneeded extra invocation of ./autogen.sh when building from @master. * flux: modify environment for Lua tests Modify Spack environment to add `./?.lua` to LUA_PATH so that fluxometer.lua can be found by tests during `make check` run from `spack install --tests all flux` * flux: fix broken flux version when on master When building @master with spack, the flux version test from `make check` fails because spack is using a shallow clone. Add a setup section for @master that calls git pull --depth=50 --tags to pull down tags and (hopefully) enough information for git-describe to work properly.
2017-11-01mfem does not use cmake for builds [anymore] - so remove code corresponding ↵Satish Balay1-10/+0
to this dependency. (#6073) This enables mfem build on OSX [with xcode/clang compilers]
2017-10-31MACSio and JSON-CWX packages (#6018)Elsa Gonsiorowski3-0/+167
2017-10-31Preinstall some llvm shared libraries so tblgen will work. (#5988)Patrick Gartung1-10/+17
2017-10-31r-somaticsignatures: created new package (#6065)Yifan Zhu1-0/+53
2017-10-31r-nloptr: Create new package. (#6063)lingnanyuan1-9/+13
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