This PR has several modifications for the r package.
- The tk package is always depended on but this pulls in X11, making the
'X' variant non-functional. This PR sets a dependency of tk on '+X'.
- There is a missing dependency on libxmu when '+X' is set.
- The libraries for R wind up in a non-standard location and are thus
left out of the RPATH settings. This PR adds that directory to RPATH.
- The MKL integer interface for gfortran is not in the BLAS libs. This
PR replaces the intel interface with the gfortran interface if needed.
- Use the `LibraryList` `ld_flags` method for blas as that is more in
line with th R Installation and Administration manual.
Note that this PR depends on PR #11956. This PR closes#8642.
TK can be built with support for libXft and X Screensaver. Both of these
are turned on in the Tk configure script. That means the system
libraries will get picked up if they are on the system and nothing is
specified in the package. Since the default for both of them is 'True' I
set the default value for the variants to 'True'.
* bowtie2: Add version 2.5.3.1 and fix to build on ARM
1. Add version 2.5.3.1.
2. Add simde for ARM.
3. Disable -fopenmp-simd when gcc 4.8.X or before for ARM.
4. Add Makefile option POPCNT_CAPABILITY=0 for ARM.
* flake8.
Fixes#11781
* Rename build log to spack-build-log.txt
* Rename environment variables file to spack-build-env.txt
* The name of the log and env files is now the same during the build
and after the build completes
* Update packages which referred to the build log/env files
* For packages installed before this commit using older names for the
build and env files, search for the older names
* ferret: use libx11 from spack
* ferret: use mpi library with or without fortran support
* ferret: add version 7.2
* ferret: no need to specify ~mpi
* ferret: creating symlinks may fail for external packages; set include/lib paths instead
* use autoreconf to regenerate configure script and config.guess for
newer architectures
* Add perl build dependency for older versions. The required perl
version is constrained because the perl script uses syntax that
is deprecated in older versions
Declare a conflict for TAU versions older than 2.28.1, that they
can't depend on libelf or libdwarf. The user can still install it
by specifying tau@2.24~libelf~libdwarf.
* py-antlr4-python3-runtime: new package
* py-antlr4-python3-runtime: fix for flake8
* py-antlr4-python3-runtime: indent docstring
* py-antlr4-python3-runtime: clarify role of this package vs ANTLR in docstring
* py-antlr4-python3-runtime: remove whitespace at end of line
The py-reportlab package includes binaries for easy_install and pip.
That blocks activation if py-setuptools and/or py-pip are installed.
This PR block the binaries from py-reportlab as easy_install and pip
should be installed with their respective packages.
* py-cf-units: new package
* py-cf-units: download from pypi.io
* py-cf-units: include py-pytest-runner as build dep
* py-cf-units: remove empty build_args function
* py-cf-units: fix for flake8
* py-cf-units: indent docstring
* py-cf-units: remove excess spaces
* py-cf-units: list master branch ahead of numeric versions
* py-cf-units: remove extension keyword from version
If R is provided by the system with a module (i.e. registered in
packages.yaml with a "module" entry) and has no discernible prefix,
this allows turbine to still make use of R.
This PR corrects a problem with the opa-psm2 package. It was
installing headers into <prefix>/usr/include and libraries into
<prefix>/usr/lib instead of <prefix>/include and <prefix>/lib.
The extra level of usr/ subdirectories causes dependent packages
like libfabric to fail to build.
The original packaging, with openfoam as a virtual and with
openfoam-com, openfoam-org and openfoam-extend as
providers, adds an obfuscation layer without any benefit.
- Rename `openfoam-com` to `openfoam`, and remove the
`openfoam` virtual package.
- `parse_anonymous_spec()` is a vestige of the days when Spack didn't
support nameless specs. We don't need it anymore because now we can
write Spec() for a spec that will match anything, and satisfies()
semantics work properly for anonymous specs.
- Delete `parse_anonymous_spec()` and replace its uses with simple calls
to the Spec() constructor.
- make then handling of when='...' specs in directives more consistent.
- clean up Spec.__contains__()
- refactor directives and tests slightly to accommodate the change.
Added a wrapperrpath variant to mpich that defaults to `True`.
Users can set this to `False` (e.g., spack install mpich~wrapperrpath) to
disable the wrapper RPATHs. This makes it easier to replacing an MPICH
installation in a container with an MPICH for the host system,
e.g., Cray MPICH with Shifter on Cori, Intel MPI, MVAPICH2, etc.
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
The version of LLVM used by flang is new enough that CppBackend doesn't exist. Unfortunately, `flang-xxxxxxxx` is seen as < `3.9.0` by the version check.
* add a special case for `flang` versions.
* OpenFOAM: rationalize architecture options
- older versions of OpenFOAM had WM_ARCH_OPTION to choose a 32-bit
build on 64-bit architectures. This is not exactly relevant anymore
and has now been largely removed from OpenFOAM.
- simultaneously the newest version of OpenFOAM has rationalized the
handling of special settings for KNL by rolling these into the
compiler options. We now do the same thing here in spack.
1. Reuse the internal variable arch_option to convey processor-specific
optimizations and add these into the C++OPT=... statement.
2. Drop spack support for configuring a 32-bit build on 64-bit
hardware.
These changes can also be applied to older OpenFOAM versions, and to
various OpenFOAM forks without issue.
* update openfoam versions. New release 1906, patched 1812 version.
ncl does not build with newer versions of gdal (or rather proj). This
also needs a small change to gdal, otherwise we end up with both proj@5
and proj@6 in the spec.
* Remove individual font-* packages and add them as resources of the
font-util package
* Update font-util package to Autotools-based package, and call
autoreconf to regenerate the old configure script
* Add font-adobe-utopia-type1
* fmt: Add cxxstd variant, plus cmake/c++ patches
Spack supported versions of fmt default to C++11 for versions
less than 5, C++14 greater than 5, with fmt implementing
fallbacks to whatever compiler supports.
To give better ABI compatibility and use of newer standards, provide
a `cxxstd` variant defaulting to 11 with 98-17 options. Use cmake_args
to set CMAKE_CXX_STANDARD as appropriate, plus use of `FMT_USE_CPP11`
option for C++98 builds. Use `conflicts` to disable use of certain
standards in versions that don't support, or fail the build, with
those standards.
Add patches to unify use of `CMAKE_CXX_STANDARD` in 3.0 versions,
remove hard-coding of compiler flags in `fmt-config.cmake`, and
prevent use of C++11 features in 4.1.0 when in supported C++98
mode.
Default to not building documents as no dependency on Doxygen is
yet present, and they are not part of the "all" build.
* Use CMake to enforce C++ standard support
Fail configure step if fmt tries to build with a cxxstd variant
not supported by the compiler (or known to CMake).
* fmt: New version 5.3.0
* The py-pytables package depends on hdf5-blosc
* Further modifications to py-pytables package
The 3.2.2 version of py-pytables should still build with internal blosc.
The issue with locking in a multithreaded environment has been
fixed/worked around in version 3.3.
Also, add bzip2 and lzo variants.
* new package/py-blessed
* make flake8 happy
* fix docstring
* tab to spaces
* Update var/spack/repos/builtin/packages/py-blessed/package.py
specify dependency version.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-blessed/package.py
specify dependency version
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add setuptools as depedency
Starting with 1.69.0, boost added a bjam option for the default symbol
visibility. Up to 1.68.0, the value was always 'global'. 1.69.0
changed the default to 'hidden' but added an option.
Most packages will work with hidden and won't notice. But some
packages may discover that an interface that they rely on is now
hidden and inaccessible.
https://boostorg.github.io/build/manual/develop/index.html#bbv2.builtin.features.visibility
For resources, it is desirable to use the expanded archive name of
the resource as the name of the directory when adding it to the root
staging area.
#11528 established 'spack-src' as the universal directory where
source files are placed, which also affected the behavior of
resources managed with Stages.
This adds a new property ('srcdir') to Stage to remember the name of
the expanded source directory, and uses this as the default name when
placing a resource directory in the root staging area.
This also:
* Ensures that downloaded sources are archived using the expanded
archive name (otherwise Spack will not be able to determine the
original directory name when using a cached archive).
* Updates working_dir context manager to guarantee restoration of
original working directory when an exception occurs
* Adds a "temp_cwd" context manager which creates a temporary
directory and sets it as the working directory
Starting with 2.1.0, backports.functools_lru_cache replaces functools32
when using python 2.7.x until python2 support is dropped in 3.0.0.
Change-Id: I8db61eac975da0042f6f5babe0f5f0c92807200e
Fixes#11526
The xfd configure script tests for libintl but incorrectly concludes
that no additional library is needed because gettext is provided in
libc. So we add '-lintl' to ldlibs to point to the Spack-installed
gettext. Note that the xfd configure script does not have a
--with-gettext option to do this for us.
Also add version 1.1.3
* xtensor-python: add version 0.23.1
* xtensor-python: update xtensor/xtl dependency version constraints
for 0.23.1
* xtensor-python: remove xtensor/xtl dependency version constraints
for the develop version to favor the latest (develop) version of
these dependencies
* xsimd: add version 7.2.3
* xtensor: add tbb variant to enable TBB parallelization
* xtensor: add version 0.20.7
* xtensor: update CMake args enable xsimd/tbb support based on
variant settings
* xtl: add version 0.6.4
* Added Cinch Spackage and updated Flecsi to Use It
Added spackage for Cinch build system and updated flecsi spackage to use
the external version of cinch
* Flake8 compliance for Cinch and Flecsi
* Fixed Cinch Issue and Requested PR Changes
Swapped cinch back to master branch rather than test branch and style
issues for PR
repeatmasker depended on HMMER but was never actually configured to
use it. The package also had many shebangs pointing to random perl
locations, now patched to use Spack's perl installation.
* Also add version 0.10.0
* Add leading '0' to 0.9.x versions (e.g. 0.09.1) and 0.8.x versions
* Don't mention acts-framework, that package isn't in Spack yet
