* opengl: make error throw on install, not fetch
* opengl: add configuration advice for darwin
* opengl: add more versions of GL/OpenGL
* opengl: improve documentation in comments
* [OpenGL] Fix formatting
* new package "DSRC" (bioinformatics)
* remove uncommented line
* get rid of unnecessary import
* convert to MakefilePackage class
* get rid of make() in install phase, remove spaces
* make flake8 happy!
Add a proper install variant for Catch(2).
This allows to use Catch2 downstram with `pkg-config` and
CMake's `find_package` commands via standard environment hints.
* fix boost and muparser for Clang 9.1.0 with C++17
* muparser: add C++11 flags
* dealii: temporary disable python by default
* dealii: make CMake find right python
* Current versions of kokkos conflict with hwloc 2.x
Current versions of kokkos cannot build with hwloc v2.x due to changes
in the associated structs. Requiring v1.11.9 for the time being
until it becomes clear what the kokkos model will be
* Explicitly commenting fix for posterity
Explicitly commented version number of hwloc dependency for kokkos for
posterity purposes and to pass code coverage for speedy merging
* Generalized Kokkos's Hwloc Dependency
Generalized dependency to v1.x of hwloc
* Fixed Flake8 issue
Fixed comment to conform to flake8
* Fixed ordering for Version Requirements
Fixed ordering to indicate <= 1.11.9, not >1
* Generalized kokkos dependency
* explicitly specify user-config.jam as it isn't found
via the environment variable on older boost versions
(cf. what debian/rules does)
=> fixes +mpi build
* fix "error: Ambiguous key" error on :1.58.999 boost
(cf. https://github.com/boostorg/boost/blob/boost-1.59.0/bootstrap.sh#L357)
* ceed bundle package including OCCA, MAGMA, Nek5000, mfem, and PETSc
Very preliminary, a lot of ad hoc decisions, fragile, missing functionality
All packages do build on my MacOS laptop with Cuda
Funded-by: ECP
Project: CEED
Time: 4 hours
Reported-by: Tzanio Kolev <kolev1@llnl.gov>
* Some adjustments in a few CEED-related packages.
This is still very preliminary, but with these changes I'm able to build from
scratch on a Mac laptop and a Linux desktop (RHEL7).
Note that there doesn't seem to be a good way to support CUDA in Spack, so
you'll have to install that manually yourself. You will also need a Fortran
compiler, in particular on a Mac where you also have to make sure that it
is being picked up in ~/.spack/darwin/compilers.yaml.
* ceed bundle package including OCCA, MAGMA, Nek5000, mfem, and PETSc
Very preliminary, a lot of ad hoc decisions, fragile, missing functionality
All packages do build on my MacOS laptop with Cuda
Funded-by: ECP
Project: CEED
Time: 4 hours
Reported-by: Tzanio Kolev <kolev1@llnl.gov>
* Reverting Mac-related CUDA checks in the OCCA and MAGMA packages.
A much better solution is to install CUDA manually and add it to
~/.spack/darwin/packages.yaml:
packages:
cuda:
paths:
cuda@8.0.54: /usr/local/cuda
* Fix flake8 warnings
Funded-by: CEED
Project: CEED/Spack
* remove unneeded commented out code
Funded-by: CEED
Project: CEED/Spack
* Don't have PETSc use MUMPS to speedup install time, try parallel installs for Magma
Funded-by: CEED
Project: CEED/Spack
* Added libceed package and made changes to get the ceed metapackage up and running.
* Get the ceed package up and running and added installing the .h file in the libceed package.
* All packages are now pointed at specific versions (either tagged or git hashed.
* Changed some of the specific versions in the CEED metapackage.
* Some version updates.
* Applied Cameron Smith's patch for the latest pumi.
* Merge
* Nek5000: Use tarball instead of git tag
* Major update of the mfem package - needs more testing. Add a testing
shell script for mfem, test_builds.sh, in the mfem directory. It builds
a number of mfem configurations to ensure they all work.
Add 'suite-sparse' variant to petsc.
Add 'develop' version of libceed.
Add 'metis' variant of laghos.
Update the dependencies of ceed.
* Changes in petsc's handling of zlib to make the latest build work on Mac.
* [MFEM] When using '+libunwind', mfem needs '-ldl'.
* [OCCA] Remove debug print statements.
* [PETSc] Replace the check ('zlib' in spec) with ('+zlib' in spec) - the
latter checks if 'zlib' variant of petsc is enabled which is incorrect;
the former checks if petsc is configured to depend on 'zlib'.
* [MFEM] Add conduit variant.
* [libCEED] Enable testing using 'make prove'.
* [MFEM] Tweak test_builds.sh - all builds pass on fedora 27.
* Add a post install test
* Add a post installation check for NekCEM
* pumi: bump git hash, remove unused patch
* Fixed testing of Laghos package
* Adding variants in CEED package
* Empty file for URL didn't work on LLNL/LC. Replacing with bundle-package.txt -> README.md.
* [MFEM] If the spec defines the 'cxxflags' compiler flags, use that value
to set the CXXFLAGS value in the mfem build system.
* Disabling HDF5 by default.
You can still build it with "spack install ceed+hdf5".
* libceed: fix use of prefix versus DESTDIR
* Added cuda variant for libCEED (off by default)
* [libCEED] When building v0.1, fix ceed.pc before installing it.
* [CEED] Add variants for OCCA and PUMI. Replace the hdf5 variant with
a variant called quickbuild that disables variants in packages to
speedup the build - currently hdf5, boost, and superlu-dist in PETSc.
* [libCEED] Remove unused 'import os'.
* [MAGMA] Add version 2.3.0.
* [OCCA] Major update of occa/package.py.
* [libCEED] Several improvements.
* [CEED] Use fixed versions for occa and libceed.
* [OCCA] Fix a bug in CUDA setup.
* NekCEM doesn't need depends_on('python')
* [OCCA,libCEED,MFEM,CEED] Update occa and libceed versions plus a few
tweaks in occa and mfem.
* Switching to gslib-1.0.2 to fix summitdev bug.
* [Nek5000] Use the Fortran 77 compiler instead of the 'fc' compiler.
Propagate any 'fflags' and 'cflags' specifications to the Nek tools.
* [MFEM] Tweak for 'ppc64le'.
* attempt to override fips compatibility error for md5
* Compiler option changes in libCEED to fix summitdev build.
* Disable the nekcem install test until it can be fixed.
* [NekCEM] Major update of the package to fix various issues.
* [NekCEM] Fix formatting
* zoltan: remove non-portable -g0 flag
the pgi compiler does not accept it
* pumi: specify dependency on cmake > 3
* [Nek5000] Add dependency on libx11 when needed. Various hacks to
support IBM XL compilers.
* [NekCEM] Link with the pthreads library - it is required.
* [MAGMA] Add a patch for magma v2.3.0 when building with gcc <= 4.8.
Add dependency on BLAS.
* [CEED] Update to magma 2.3.0. When building with gcc < 4.9 constrain
the used suite-sparse version to <= 5.1.0 - starting with v5.2.0,
suite-sparse requires gcc >= 4.9.
* Small updates
* [libceed, gslib] Fix style
* [Nek5000] Need 'libxt' as a dependency as well.
* [MUMPS] Temporary workaround for ray.
* Updating occa and libceed to laters pre-1.0.0 and pre-0.2 hashes
* petsc: add pkg-config patch for variable quoting
Variable definitions in pkg-config are processed more like make than a
shell, so don't need quoting. Older versions of pkg-config (<= 0.28)
did not remove the quotes when printing the value.
Freedesktop #67904 (https://bugs.freedesktop.org/show_bug.cgi?id=67904)
Reported-by: Tzanio Kolev <kolev1@llnl.gov>
* petsc: add 3.8.4 and myself as co-maintainer
* Updating libceed to latest pre-0.2 hash.
* [PETSc] Add the 'headers' and 'libs' properties.
* [MFEM] Explicitly add rpaths to link flags for external packages.
This is necessary when MFEM's exported options (in config.mk) are
used outside of Spack for linking against MFEM.
* Unset MFEM_DIR before building MFEM
* [PETSc] As observed by @jedbrown, there is no need to define the 'libs'
property explicitly - the default handler works fine too.
* Build MAGMA shared by default, install a few additional headers
* Forgot a self
* Switching to OCCA tag v1.0.0-alpha.4.
Adding urls for OCCA and libCEED ('spack uninstall' complains otherwise).
* Removed FIXMEs for OCCA tag
* [occa] Cleaned up tagged versions
* [libceed] Updated occa to v1.0.0-alpha.5
* [ceed] Updated occa to v1.0.0-alpha.5
* [libCEED] Always define the 'NDEBUG' makefile option based on the
'debug' variant setting - this should always work regardless of the
default setting inside the libceed makefile.
* [MUMPS] Revert a temporary workaround.
* [CEED, libCEED] Minor tweaks.
* libCEED v0.2 release
* [CEED] Use version 0.2 of libCEED.
* [HPGMG] Remove duplicate version.
* [CEED] Update the hpgmg version
* hpgmg: use tarball for 0.3
The Git repository contains somewhat heavy documentation so the tarballs
are much faster.
* hpgmg: +fe was default for the 0.3 release
* hpgmg: explicitly name build directory to avoid use of ambient PETSC_ARCH
* [HPGMG] Fix flake8 formatting
* libceed@0.2: work around occaFree issue
* Add ignore_conflicts to package activation
includes:
* with_dependency flag for do_activate
* ignore_conflicts flag for do_activate
* start of cleanup of activate cmd
* ensure that apr is picked up
* Update package.py
* add apr explicitly as dependency
* remove unnecessary newlines
* Update package.py
fixing dependencies
Modifications:
* Added zlib dependency, starting from version 3.0.0
* Added memchecker support for debugging
* Remove mpirun and similar links if slurm is selected as a scheduler
* [hypre] Add the 'headers' property plus a small tweak in the 'libs'
property.
* [hypre] Add fallbacks for searching for '.libs' in 'prefix.lib64' and
in all of 'prefix'.
* [hypre] Fix style.
* [hypre] Use find_headers instead of find + HeaderList.
* added a new package file for PHIST (Pipelined, Hybrid-parallel Iterative Solver Toolkit)
* packages/phist: fix some formatting errors (too long lines etc)
and set allowed values for option "outlev"
* packages/phist: fix some more flake8 errors
* add headers property to netlib-lapack and intel-mkl
* ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())
* added a new package file for PHIST (Pipelined, Hybrid-parallel Iterative Solver Toolkit)
* packages/phist: fix some formatting errors (too long lines etc)
and set allowed values for option "outlev"
* packages/phist: fix some more flake8 errors
* phist: use headers property to find lapacke include dir
* phist: fix flake8 error
* phist: be more specific about dependencies and update version
* phist: state trilinos minimum version when building with Tpetra kernels
* gmp: add oldish version 5.1.3 with checksum
* phist: get rid of the 'petsc+complex' variant, it can be installed by kernel_lib=petsc ^petsc+complex
* phist: new version
* phist: fix version checksum
* Revert "add headers property to netlib-lapack and intel-mkl"
This reverts commit d8cb62905ebfb2cba186fd2d736d54a88a49d089.
* Revert "ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())"
This reverts commit d406a77ed7879c124fbaf1d757d002b9f0771620.
* phist: remove unused function
* phist: reorder package file versions/variants/depends_on/rest
* phist: some minor changes requested by @adamjsteward
* Add latest version of MPFR and patches for older versions
* Fetch and checksum patches instead of storing them
* Fix bug, version attribute was being overridden
* meme: added perl-xml-parser dependency, resolved issue. still need to fix ghostscript or image-magick, conversion not working.
* meme: fixed issue with libxslt/libxml2 conflict, and added imagemagick support
* meme: removing libxslt/libxml2 dependency lines
* meme: configure args
* meme: separating configure args
* meme: removing a comment, and hoping for travis to rebuild. site seems back up.
* meme: make image-magick optional
* meme: add comment referencing PR
* meme: bah flake8
* Promote to Autotools for simplicity; broaden Intel CPU opt targeting from SSE4.2 to AVX2
* make Intel CPU opt targeting same as in ../libxc
* flake8 W291
* use canonical means to pass (ahem) the test phase, h/t @adamjstewart
* revert f25d598 (unrelated merge)
* re-merge
* make py-setuptools a run-time-only dep for py-basemap and patch python package to only apply setuptools flag for build deps
* py-qtconsole does not require setuptools
* intel-xed: new package
The Intel X86 Encoder Decoder library for encoding and decoding
x86 machine instructions.
* intel-xed: style fixes for flake8.
* intel-xed: better style fix
* intel-xed: update to version 2018.02.14, add PYTHONPATH for
building with python 3, cleanup the opt flag.
The restrict compilation option with icc causes deadlock when multithreading is used. This issue has already been reported to the Scotch development team, but for current versions it is more reliable not to use the restrict compilation option.
* libtool: actually do symlinking correctly on darwin
Version 4 of the libtool/darwin debacle:
AutotoolsPackage hardcodes libtool & libtoolize into the autoreconf
stage, so the commands `libtool` and `libtoolize` MUST be present, and
shimming in glibtoolize into AutotoolsPackage when sys.platfrom ==
'darwin' does not work.
join_path(spec['libtool'].prefix.bin, 'libtool') still shadows system
BSD libtool (in apple-cctools, see PR #7177), but this shadowing could
be okay, depending on the combination of dependent specs.
* librom: new package
* Adding unzip package.
* Removing bzip2 dependency in unzip and raising an error when on Cray.
* Fixing error.
* Using conflicts statement for Cray detection in unzip package.
* add headers property to netlib-lapack and intel-mkl
* ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())
* fix flake8 errors
* ghost: remove unnecessary query parameter
* fix flake8 errors
* ghost: make it a CudaPackage (as suggested by @davydden, thanks!)
* ghost: missing whitespace
* Fix a bug when checking for 'xl' or 'xl_r' compiler.
* Add support for parallel build - the 's', 'c', 'd', and 'z' targets
are build separately allowing parallel builds.
* When build '+shared', inject all dependencies into the link lines of
the mumps libraries.
* Run the examples only when installing with the '--test' Spack option.
It seems there has been a change in concretization that resulted in
a request for a llvm latest (5.0.1) while not satisfying the later
more precise request for a version.
Remove the first line and only rely on the last.
A build of python@3.X had the following in the logs:
```
The necessary bits to build these optional modules were not found:
_dbm _gdbm _tkinter
```
As Tkinter is already a variant, we adopt the same strategy for dbm.
This includes:
* Added latest available versions (1.11.9, 2.0.0)
* Added variants to enable graphical output from lstopo
* Enabled build of the bundled netloc package if @2.0.0:
* Added dependency from numactl if @:1.11.9
* Added a constraint to avoid using hwloc@2.0.0 with openmpi
cube's configure only recognizes qt versions with single digit version
components and breaks with qt 5.10. Patch the configure files directly
to avoid having to regenerate them.
Mscgen is a small program that parses Message Sequence Chart descriptions and
produces PNG, SVG, EPS or server side image maps (ismaps) as the output.
See http://www.mcternan.me.uk/mscgen/
This is needed when using system lua on RHEL and clones where lua
is installed in /usr/lib64. Note that the path entry for lua in
packages.yaml should specify the major/minor version of lua (since
this is used to calculate the lua lib directory)
updated hoomd-blue to latest tagged release in repo. This version also supports newer gcc6 compilers, so added constraint for older version to avoid breaking existing installs.
+ Newer versions of zoltan2 are doing test compiles that link to parmetis. If
these checks don't find `metis.h`, the check fails.
+ This small tweak ensures that the zoltan2 configure step can find `metis.h`
that is provided by spack.
For hdf5 `1.8.10` and some compilers, the hdf5 build system adds the
'-ansi' flag. hdf5 1.8.10 is not actually ansi compliant so this
adds a patch to modify the places where it violates ansi
compatibility (which ends up being a few comments).
Make neuron package more generic
* find the bin directory dynamically for use in run_env and spack_env
* replace filter_compilers after install with filter_compiler_wrappers
* update checksum for _current_ 7.5 version
* make +python conflict with ~shared
* prepend the architecture specific lib directory to the LD_LIBRARY_PATH
Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
Fix installs as "root" user for the last libSplash release.
Missing quoting of string compares resulted in a CMake error
when run as root (e.g. in a Docker build).
This updates Cray.setup_platform_environment to use cray-specific
pkgconfig paths so that all providers of 'pkgconfig' have access
to them (previously the 'pkg-config' provider had this but the
'pkgconf' provider did not).
* [OpenMPI] Add the 'headers' property. This removes some redundant
headers from sub-directories, returned by the default '.headers'
handler.
* [OpenMPI] In the .headers property, add a fallback to search all of
prefix for the mpi.h header. Recommended by @junghans to support some
external configurations, see #7268.
* add verilator package
* try to add environment variable and include folder
* manually install existing scripts and patch out spack's CXX wrapper
* added some comments
* make flake8 happy
Adds Google's new cpu_features library.
Install was added recently, so don't take the `0.1.0` release but
the current `master` until a new version is published.
* Combined llvm and llvm-lld: removed the separate llvm-lld package
and added llvm-lld as an optional add on to the llvm package (the
way several other llvm tools are maintained e.g. lldb)
* Added more lld hashes to llvm package
* The 'CppBackend' target doesn't exist for version 3.9.0 or later
so exclude it for later versions
* Was incorrectly specifying 'sparc' as a target for the 'sparc'
architecture - needed to specify 'Sparc'
* Fix issue #7248 building llvm: don't make the LLVMDemangle target
for llvm < 4.0.0
* No longer need to patch CMake. Using CMAKE_CXX_FLAGS to include BLAS/LAPACK/MKL header files properly.
* Backport two patches to QMCPACK versions prior to 3.3.0: https://github.com/QMCPACK/qmcpack/pull/621, https://github.com/QMCPACK/qmcpack/pull/623
* Insufficient to include lapack_dir in CMAKE_CXX_FLAGS, CMAKE_C_FLAGS is also needed.
* Make patched Espresso a default variant instead of a hard dependency. This is easier on computer architectures where Espresso is hard to build.
* Fix patching with QE variant. Now using correct form of patch command.
* Add QMCPACK v3.4.0
* Backport patch to QMCPACK versions prior to 3.3.0: https://github.com/QMCPACK/qmcpack/pull/643
Yaml-cpp hasn't tagged a release in over 2 years, yet they have fixed
many things and now have the ability to use find_package in CMake.
Since we use this feature in Nalu, we require the latest yaml-cpp
until they tag a new release. I have also deprecated the now
unnecessary ENABLE_INSTALL flag.
* Added a package for the MDAnalysis toolkit.
* Adding a package for the Python virtualenvwrapper pacakge. Included
dependent virtualenv-clone and stevedore packages. Updated py-pbr with
a new version to support this.
* Added extra necessary dependencies and fixed the file download paths.
* Added a package for the MDAnalysis toolkit.
* Added a new package for pygpu, which is the python front end of the
libgpuarray. Additionally changed the dependency for theano so that
it properly picks up the pygpu library.
* Added the libcheck package. Fixed flake8 errors in py-pygpu recipe
and removed spurious dependency on cudnn for libgpuarray.
The edit phase of cbench was used to set environment variables. Though
this works, the variables set this way are not dumped to build.env.
This commit fixes the issue by setting those variables in the
`setup_environment` function.
* [SUNDIALS] Add the 'headers' and 'libs' properties, plus a couple of
small tweaks.
* [SUNDIALS] Revert incorrectly changed conflicts() directive. Fix style.
Fixes#5189
When working with non-normalized paths containing ".." on some
file systems, Spack was found to encounter a permission error when
writing to the path. This normalizes a path written by the
intel-parallel-studio package and also normalizes all paths
written by the license install hook (for all packages) to avoid
this issue for intel-parallel-studio.
Adds the first stable API release of ADIOS2, v.2.1.0.
Also adds a missing `pybind11` CMake flag for proper Python
selection (needed in both the new and previous version).
To accommodate build systems on Darwin which look for glibtool/ize,
#7060 attempted to provide glibtool/ize symlinks for libtool/ize
but accidentally created the same symlink twice. #7073 reverted this
and replaced libtool/ize with glibtool/ize on Darwin. This led to
#7163 since AutotoolsPackages depend on the presence of the 'libtool'
binary, so this returns to the approach of #7160 but makes the
correct symlinks.
XBraid installs `libbraid.a`, but the default `libs` method
implementation will search for `libxbraid`, which does not exist. This
commit fixes the behavior of the `libs` method for the `xbraid`
package by overriding package's `libs` method.
Prior to this commit, running `spack module refresh` with `gdbm`
installed throws the warning:
```console
==> Warning: Could not write module file [/Users/oxberry1/spack/share/spack/lmod/darwin-sierra-x86_64/Core/gdbm/1.14.1.lua]
==> Warning: --> global name 'spack_cc' is not defined <--
```
This warning is repeated for every `gdbm` installation in Spack.
The cause of the issue seems to be the same as in spack/spack (#6089):
using `spack_cc`, `spack_cxx`, or similar inside `configure_args`
causes the warnings to throw when module files are generated.
Moving the use of `spack_cc` into `setup_environment` seems to fix the
problem, even though it's a bit of a kludge.
Running `spack module refresh -m lmod --delete-tree -y` throws the
following warning:
```console
==> Warning: Could not write module file [/Users/oxberry1/spack/share/spack/lmod/darwin-sierra-x86_64/openblas/0.2.20-ibhtl5q/clang/5.0.1/ipopt/3.12.9.lua]
==> Warning: --> global name 'prefix' is not defined <--
```
This warning arises because the variable expansions in
`spack.modules.BaseFileWriter` occur at module/package scope. Even
though `prefix` is an argument to `install` methods in e.g.,
`MakefilePackage`, so using this argument within package methods is
legal, doing so defeats the introspection logic in
`spack.modules.BaseFileWriter`. Replacing `prefix` with `self.prefix`
resolves the problem, because the introspection logic in
`spack.modules.BaseFileWriter` can use introspection to query IPOPT's
prefix.
Following the discussion with Todd and Adam, find has been modified to
accept glob expressions. This should not affect performance as every
glob implementation I inspected has 3 cases (no wildcard, wildcard but
no directories involved, wildcard and directories involved) and uses
fnmatch underneath.
Mixins have been changed to do by default a non-recursive search (but
a recursive search can still be triggered using the recursive keyword).
Following a comment from Todd, the search path for the files listed in
`filter_compiler_wrappers` can now be narrowed. Anyhow, the function
implementation still makes use of `find`, the rationale being that we
have already seen packages that install artifacts in e.g. architecture
dependent folders. The possibility to have a relative search path might
be a good compromise between the previous approach and the one suggested
in the review.
Also: 'ignore_absent' and 'backup' keyword arguments can be optionally
forwarded to `filter_file`.
Implemented a declarative syntax for the additional behavior that can
get attached to classes. Implemented a function to filter compiler
wrappers that uses the mechanism above.
* Remove variants disabling blas and lapack for py-numpy, issues
building these have been resolved
* For CMake greater than 3.10, FindMPI changed, so use
MPIEXE_EXECUTABLE instead of MPIEXE for 3.10 and newer
fixes#7128
Before this PR packages that were indirectly dependent on python might
have failed due to inconsistency between the python found in the
environment and the standard libraries set in PYTHONHOME
This adds a static version of hpgmg (up to now only the latest commit
from the master branch was available). This also adds a debug variant
and sets optimization flags for ~debug when the compiler is gcc,
intel, or clang
Adds the latest release of libSplash (1.7.0) and newly learned
CMake flags for explicit dependency control.
Modifies HDF5 dependency: non-MPI splash does (and did) never run
with a parallel HDF5, due to it's internal cross-dependencies on
MPI.
* libdwarf: fix linker flags
* libdwarf: fix header install names
* libdwarf: add zlib dependency
Prior to this commit, libdwarf was linked to the system zlib. This
commit links it to spack-installed zlib.
* libdwarf: fix dynamic library suffix for Darwin
* Adding support for the Accelerate library on OS X
* Fixed guard on variable and added another depends_on statement to make sure that openblas gets selected even when openmp_blas variant is not turned on.
* Added a package for the MDAnalysis toolkit.
* Added some flags to fix the build RPATHs and OpenMP for LBANN on OS X.
* Fixed Hydrogen branch of Elemental to find OpenMP on OS X.
* 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
