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2018-01-29Mark slow unit tests (#6994)Massimiliano Culpo16-72/+193
* Marking database tests as slow * Marking url command tests as slow * Marking every test that uses database as slow * Marking tests that import files as slow * Marking gpg tests as slow * Marking all versions and one list tests as slow * Added more markers to unit tests + cli option to skip slow tests Following a discussion with Axel, the generic 'slowtest' marker has been split into 'db', 'network' and 'maybeslow'. A brief description of the meaning of each marker has been added to pytest.ini. A command line option to run only fast tests has been added to 'spack test' * Don't use classes to group tests together Reverted grouping tests under a class, as required in the review * Minor style changes
2018-01-28Remove Package instance caching in Repo (#6367)scheibelp9-60/+27
This attempts to address one of the complaints at #5996 (comment): > Repo currently caches package instances by Spec, and those Package instances have a Spec. > This is unnecessary and causes confusion. I think I thought that we'd need to cache instances > after loading package classes, but really just caching the classes is fine. With this update, Repo's package cache is removed and Specs cache the package reference themselves. One consequence is that Specs which compare as equal will store separate instances of a Package class (not doing this creates issues for #4595 (comment)). There were several references to Spec.package that could be replaced with Spec.package_class without any additional modifications. There are still a couple remaining references to Spec.package in Spec that would require adding functionality before replacing (e.g. calling Package.provides and Package.installed). Note this makes it difficult to mock fetchers for tests which invokes code that reconstructs specs. test_packaging was one example of this where the updates caused a failure (in that case the error was avoided by not making an unnecessary call). Details: * Replace instances of spec.package with spec.package_class where a class method is being called * Remove instances of Repo.get where Spec.package_class can be used in its place * remove Repo.get caching instances of Package class for specs * remove redundant check (which is also incorrect now that each spec stores its own copy of its package) * avoid creating mirror with specs because it copies specs and those copies dont refer to the mocked fetcher (and it is also not required for the test) * remove checks that are no longer necessary since repo doesn't cache specs
2018-01-28Fix gfortran 7 detection (#7017)Adam J. Stewart4-7/+44
2018-01-28Cleaned up JUnit report generation on install (#6977)Massimiliano Culpo5-226/+477
* Cleaned up JUnit report generation on install The generation of a JUnit report was previously part of the install command. This commit factors the logic into its own module, and uses a template for the generation of the report. It also improves report generation, that now can deal with multiple specs installed at once. Finally, extending the list of supported formats is much easier than before, as it entails just writing a new template. * Polished report generation + added tests for failures and errors The generation of a JUnit report has been polished, so that the stacktrace is correctly displayed with Jenkins JUnit plugin. Standard error is still not used. Added unit tests to cover for installation failures and installation errors.
2018-01-28libtool, binutils: fix darwin linking (#7073)Geoffrey Oxberry2-7/+12
* libtool: fix linking of libtool on darwin * binutils, libtool: fix conflicts w/ BSD tools, v2 Fix namespace conflicts with BSD tools in a more elegant fashion, using a program prefix, similar to Homebrew.
2018-01-26Tell R's configure about tcltk config (#7085)George Hartzell1-1/+6
* Tell R's configure about tcltk config Add configure arguments that specify the location of the tcl and tk config scripts. Fixes #7072 * Flake8 cleanup
2018-01-26new package: essl (#6335)Brian Van Essen2-2/+106
Added support for the IBM ESSL math library.Updated Elemental to be able to build with ESSL.
2018-01-26Bzip2 now uses 'spack_cc' as a compiler, instead of plain 'cc' (#7074)Massimiliano Culpo1-2/+4
Looking at build logs, it seems that prior to this commit bzip2 was using 'cc', and relying on the PATH to be set correctly to find Spack wrappers. This commit improves the robustness of the recipe, by using the absolute path of the wrapper.
2018-01-26Enable install of multiple specs from yaml files (#6984)Federico Ficarelli2-21/+52
2018-01-25Protobuf package: allow building shared library (#7067)Brian Van Essen1-0/+4
This adds a +shared variant for building shared libraries in the protobuf package and enables it by default.
2018-01-25Lbann package: bug fix (#7066)Brian Van Essen1-2/+2
Fixed a bug in the guard on cub functionality. Reduced the requirements on hwloc to make it simpler to build on Power systems.
2018-01-25Python Installs: No User Site Dir (#7065)Axel Huebl1-3/+3
Avoid adding an "outside" (local home's) python user site directory during python package installs. Implements #6611 Fixes packages with auto-find side effects such as `py-setuptools` that cause `py-matplotlib` to fail to build #6558
2018-01-24libtool: symlink libtool{ize} to glibtool{ize} (#7060)Geoffrey Oxberry1-3/+19
On Darwin and other BSD systems, the system 'libtool' and 'libtoolize' are BSD libtool and libtoolize, respectively. Some build systems require the GNU versions of these commands, so BSD package systems tend to name the GNU versions 'glibtool' and 'glibtoolize', respectively, to avoid namespace collisions. A problem with the current libtool package is that it installs the GNU libtool commands as 'libtool' and 'libtoolize', respectively, but build systems on BSD platforms will attempt to run 'glibtool' and 'glibtoolize'. The expedient solution to this problem is to symlink 'libtool' to 'glibtool' and 'libtoolize' to 'glibtoolize', because attempting to patch the detection logic one build system at a time seems impractical.
2018-01-24netlib-xblas 1.0.248: new package (#7024)Geoffrey Oxberry2-0/+100
* netlib-xblas@1.0.248: new package * netlib-lapack: add xblas option
2018-01-23Lbann update (#6987)Brian Van Essen2-18/+57
* Added new link line flag * Refactored some of the common components out of the different version's build commands. Also corrected the when commands to properly capture non-numeric names such as local. * Added support to the Elemental package for the Hydrogen branch.
2018-01-23Fix gtkplus build by hardcoding X11 support (#6971)Federico Ficarelli7-16/+14
* Fix gtkplus build by hardcoding X11 support * Remove +X variant from gtkplus dependents
2018-01-23Fix +readline handling (#7048)Federico Ficarelli1-4/+2
2018-01-23argp-standalone@1.3: new package (#7014)Geoffrey Oxberry2-0/+61
Adds a package for the standalone version of the argp argument parsing interface from glibc for unix-style command options.
2018-01-23Fix error message typo in 'spack create' cmd (#7042)Alastair Harrison1-1/+1
- Previously would print the spec's namespace twice, rather than printing the spec's namespace, followed by the repo's namespace.
2018-01-23new package: gslib (#6328)Thilina Rathnayake1-0/+90
2018-01-23Fix GEANT4 and make more portable and flexible (#6956)Benedikt Riedel4-14/+90
* Turning off default Qt support. Restricting Qt version to <= 4.9 else geant4 won't build * Making vecgeom optional * Differentiating between cxx11 and cxx14 support * Making vecgeom optional. Part 2. forgot to move usolids option * Adding explicit CXX11 and CXX14 support * Adding more clhep version to support newer GEANT4 versions * Adding GEANT4 versions 10.03.p03 and 10.04 * Checkpoint. Adding opengl and x11 variant. Lead up to more changes to enable X11 support * Adding dependency on fixesproto for newer versions * Making the X11 dependent pieces work without requiring X11 on the system * Adding motif
2018-01-23netlib-lapack: add versions 3.7.0, 3.7.1, 3.8.0 (#7025)Geoffrey Oxberry1-0/+4
2018-01-23A new package: log4cplus. (#7015)健美猫1-0/+36
2018-01-23Version update for cfitsio (#7032)Marty McFadden1-1/+2
2018-01-23r-snprelate: new package (#7036)Yifan Zhu1-0/+52
2018-01-23r-gdsfmt: new package (#7035)Yifan Zhu1-0/+47
2018-01-22Update gl/qt options for vtk package (#6551)Scott Wittenburg5-22/+168
This provides options for hardware and software rendering with the gl API and updates the vtk package to make use of those options: * Create new "gl" virtual package, provided by mesa * Add external-only "opengl" package, which represents a system install that provides gl * For vtk: prefer system gl implementation by default to get speed up from hardware rendering. When software rendering is specifically requested (+osmesa), try to use the llvmpipe approach, as it is much faster. * Make qt dependency optional for vtk * Add basic support for VTK on osx * qt: Depend on virtual gl package, rather than mesa impl
2018-01-22Version update for 2.22 (#7023)Kelly (KT) Thompson1-0/+1
2018-01-22perl-graph: Create new package (#7022)Eric1-0/+36
2018-01-22perl-array-utils: Create new package (#7020)Eric1-0/+34
2018-01-22perl-app-cmd: Create new package (#7019)Eric1-0/+34
2018-01-22perl-perlio-gzip: Create new package (#7018)Eric1-0/+35
2018-01-21Visit 2.13.0 (#6947)Geoffrey Oxberry1-4/+13
* visit: add version 2.12.3 * visit: add version 2.13.0 * visit: enable building with hdf5+mpi * visit: add qwt dependency Building VisIt requires Qwt, which is not part of Qt. Prior to this commit, this dependency was not included in the VisIt spack package, resulting in a configure-time bug with an error message indicating a missing Qwt dependency. This commit fixes this bug by adding Qwt dependency information.
2018-01-21LIBXSMM 1.8.2 (#6896)Hans Pabst1-24/+25
* Included LIBXSMM 1.8 into the list of available versions. * LIBXSMM 1.8.1 * LIBXSMM 1.8.2 (release notes: https://github.com/hfp/libxsmm/releases/tag/1.8.2). * LIBXSMM: Use join_path instead of hard-coding the separator. Install "version.txt" into the documentation directory. Removed installing "README.md" from LIBXSMM's root directory as it overrides README.md provided there. The latter uses correct relative references to the other documentation parts. Note: Apparently, "FC=/path/to/gfortran spack install libxsmm" is currently needed for Spack since does not pick-up the Fortran compiler (but incorrectly uses the C compiler instead). * LIBXSMM: converted Package into MakefilePackage (to address https://github.com/spack/spack/pull/6896#discussion_r160993923). * LIBXSMM: account for changed file set in 1.8.2 onward (addresses https://github.com/spack/spack/pull/6896#pullrequestreview-88670974). * Fixed incorrect behavior of "+header-only", which did not install the "src" folder. Addressed https://github.com/spack/spack/pull/6896#discussion_r162783180 and https://github.com/spack/spack/pull/6896#discussion_r162783221. * Use conflicts msg argument to present a friendly error message.
2018-01-20dealii: update CMake dependency (#7010)Denis Davydov1-2/+2
2018-01-20Added libgit2@0.26.0 (#6952)sknigh1-0/+1
2018-01-20Added added libssh2@1.8.0 (#6951)sknigh1-0/+1
2018-01-20flex: restrict GCC conflict to newer Ubuntu releases (#6963)Michael Kuhn1-2/+2
flex 2.6.4 compiles fine with GCC 7 on (at least) Ubuntu 16.04 and Fedora 27.
2018-01-20llvm: add version 5.0.1 (#6957)Geoffrey Oxberry1-0/+15
2018-01-20gtkplus: Update to 2.24.32 (#6964)Michael Kuhn1-0/+1
2018-01-20r-getopt: new package (#6973)Yifan Zhu1-0/+39
2018-01-20ipopt: add version 3.12.9 (#6982)Geoffrey Oxberry1-0/+1
2018-01-20perl-list-moreutils: Create new package (#6997)Eric1-0/+34
2018-01-20sniffles: add version 1.0.7 (#7004)peetsv1-0/+1
2018-01-20A new package: lumpy-sv. (#7009)健美猫1-0/+43
2018-01-20Add Abinit 8.6.3 (#6959)Ondřej Čertík1-1/+2
2018-01-20Add boost 1.66.0 (#7000)Bruno Turcksin1-0/+2
2018-01-20Restore multiprocessing in unit tests (#6949)Massimiliano Culpo4-9/+2
* Revert "Travis: use --concurrency=multiprocessing only on build tests (#6872)" This reverts commit 596d463714d46929f81db62b171c5a772679bb12. * Removing 'coverage combine' in test script According to what was discovered in #6887, one of the problems is calling 'coverage combine' twice without the '-a' flag. This removes the first call within our test scripts.
2018-01-20qt@4 : update corewlan patch for OS X 10.1[23] (#6943)Geoffrey Oxberry1-5/+5
Update the qt4 CoreWLAN patch to apply to macOS/OS X 10.12 and 10.13, which both still use the CoreWLAN framework in their SDKs (although it's apparently deprecated?!). Without this patch update, `spack install qt@4.8.6` fails on macOS/OS X 10.12 because the linker cannot find headers from the CoreWLAN framework.
2018-01-19vtk@:6.1.0 : disable Obj-C gc for XCode >= 5.1Geoffrey Malcolm Oxberry1-0/+12
Apple removed support for Objective-C garbage collection in binaries in XCode 5.1, but VTK 6.1.0 and earlier set flags for garbage collection, resulting in a compile-time bug when compiling VTK using any recent version of XCode (i.e., Apple Clang). This commit fixes this bug by removing the garbage collection flags via setting the variable `VTK_REQUIRED_OBJCXX_FLAGS` to the empty string. This variable has the same value (i.e., the empty string) in the root-level CMakeLists.txt file for VTK 6.2.0 and later.