Some R packages require access to a home directory to pass install tests. Extend
r-modules to allow creating a temporary home directory for packages with
such requirements.
r-modules: fix r package system dependencies
r-modules: fix terra package dependencies
r-modules: fix edge case for R package import
The R package "import" has a name that clashes
with the nix function "import". The package
name in nixpkgs is correctly modified to
avoid the clash, but the name of the
R package was also being changed in
cran-packages.nix, which broke downloading
of the package.
cran-packages.nix has been manually patched,
and genreate-r-packages.R has been fixed so
future automatic updates will succeed.
r-modules: fix repeated `pkgs.` and svglite
Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
{
mpi = super.mpich;
}
All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
continuation of #109595
pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.
python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
rzmq uses pkgconfig.
clustermq now incorporates ZMQ libs directly, rather than using
the rzmq package. clustermq now uses zeromq and pkgconfig.
Both packages needed patchShebangs, due to pkgconfig.
`data.table` had a `postInstall` step to rename `data.table.so` to `datatable.so`, but after the package bump the file was already called `datatable.so` and `mv` command would fail.
The last snapshot was 4 months ago (2020-08-19). I also found that I needed newer definitions when I was trying to fix the R arrow package.
This update required a couple of manual changes:
1. Removing a few deleted packages from default.nix
2. Renaming the "assert" package to "r_assert" in generate-r-packages.R because "assert" is a keyword in Nix
