* 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

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

* 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.

* 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.

* 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

Added support for the IBM ESSL math library.Updated Elemental to be
able to build with ESSL.

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.

This adds a +shared variant for building shared libraries in the
protobuf package and enables it by default.

Fixed a bug in the guard on cub functionality.  Reduced the
requirements on hwloc to make it simpler to build on Power systems.

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

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.

* netlib-xblas@1.0.248: new package

* netlib-lapack: add xblas option

* 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.

* Fix gtkplus build by hardcoding X11 support

* Remove +X variant from gtkplus dependents

Adds a package for the standalone version of the argp argument parsing
interface from glibc for unix-style command options.

- Previously would print the spec's namespace twice, rather
  than printing the spec's namespace, followed by the repo's namespace.

* 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

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

* 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.

* 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.

flex 2.6.4 compiles fine with GCC 7 on (at least) Ubuntu 16.04 and Fedora 27.