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
- Fix a bug introdcued by removing parse_anonymous_spec()
- Conflicts' when specs are now *actually* anonymous, and the name of the
package is implicit, so we need to remember to add it back to error
messages.
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.
- Add set -u to the setup-env.sh test script
- Refactor lines in setup-env.sh that tested potentially undefined
variables to use the `[ -z ${var+x} ]` construct
- tests use a shell-script harness and test all Spack commands that
require special shell support.
- tests work in bash, zsh, and dash
- run setup-env.sh tests on macos and linux builds.
- we run them on macos and linux
- replace use of [[ with [
- replace function foo { .. } with foo() { .. }
- wrap some long lines
- add lsof and /proc/fd magic so that we can find the sourced file even in dash
- only do the complicated shell checks in one place; test $_sp_shell
elsewhere.
* 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.
- There's too much information on our PRs, and the Travis test results
(which are arguably more important than coverage) get buried in
coverage information
- Remove coverage sub-categories, as you can browse codecov's file view
to see roughly the same thing
- show only project/patch on GitHub PRs.
* 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.
