rstudio: 1.4.1717 -> 2022.02.3+492
The old version does not compile with gcc11. Also the used nixos-22.05
libraries (R interpreter) have changed their interfaces that have to be
also patched. Updating RStudio is useful.
* Remove Quarto patch
Follow review in
https://github.com/NixOS/nixpkgs/pull/177021#pullrequestreview-1007625773
* Fix not FHS paths
Create explicit nix path replacement of hard coded FHS paths for pandoc and nodejs.
* lib/strings: optimise hasInfix function
* lib/strings: optimise hasInfix further using regex
* rstudio: call hasInfix with a string
* lib/strings: remove let from hasInfix
Co-authored-by: pennae <82953136+pennae@users.noreply.github.com>
Co-authored-by: pennae <82953136+pennae@users.noreply.github.com>
Co-authored-by: Justin Bedo <cu@cua0.org>
Co-authored-by: Jonathan Ringer <jonringer@users.noreply.github.com>
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
Co-authored-by: Benjamin Darwin <bcdarwin@gmail.com>
Also begin to start work on cross compilation, though that will have to
be finished later.
The patches are based on the first version of
https://reviews.llvm.org/D99484. It's very annoying to do the
back-porting but the review has uncovered nothing super major so I'm
fine sticking with what I've got.
Beyond making the outputs work, I also strove to re-sync the packages,
as they have been drifting pointlessly apart for some time.
----
Other misc notes, highly incomplete
- lvm-config-native and llvm-config are put in `dev` because they are
tools just for build time.
- Clang no longer has an lld dep. That was introduced in
db29857eb3, but if clang needs help
finding lld when it is used we should just pass it flags / put in the
resource dir. Providing it at build time increases critical path
length for no good reason.
----
A note on `nativeCC`:
`stdenv` takes tools from the previous stage, so:
1. `pkgsBuildBuild`: `(?1, x, x)`
2. `pkgsBuildBuild.stdenv.cc`: `(?0, ?1, x)`
while:
1. `pkgsBuildBuild`: `(?1, x, x)`
2. `pkgsBuildBuild.targetPackages`: `(x, x, ?2)`
3. `pkgsBuildBuild.targetPackages.stdenv.cc`: `(?1, x, x)`
This attempts to fix the issue described at
https://github.com/NixOS/nixpkgs/pull/22219#issuecomment-291801133.
Any change to the custom packages passed to RStudio causes this to
completely rebuild RStudio, which is completely unnecessary and also a
bit of a hindrance as it's a fairly slow build.
This rolls back most of that old PR, and instead implements something
more like rWrapper. Existing configurations with the old useRPackages
will break.
https://nixos.org/nixpkgs/manual/#r-packages contains a method for
setting up an R environment with a specific set of libraries, and it
creates an R wrapper which points R to those libraries.
The package RStudio relies on the standard R package, which then
cannot access any of the libraries specified in a custom R
environment. While one may easily use pkgs.rstudio.override to change
rstudio's R dependency to the custom R environment, this accomplishes
nothing because while RStudio runs the correct R wrapper it clears out
the environment variable R_LIBS_SITE - and so it is still unable to
use any of those packages.
In order to work around this problem, these changes allow the user to
optionally modify rstudio's wrapper to set environment variable
R_PROFILE_USER to an R script which sets R's .libPaths(..) to point to
the same libraries; that script is generated from R_LIBS_SITE in the R
wrapper.
By default, this change has no effect. If R is overridden to
something else, and if useRPackages is changed from its default of
false, then the change described above is made; for instance:
{
packageOverrides = pkgs: let self = pkgs.pkgs; in
rec {
rEnv = pkgs.rWrapper.override {
packages = with self.rPackages; [
dplyr ggplot2 e1071 rpart reshape
];
};
rstudioEnv = pkgs.rstudio.override { R = rEnv; useRPackages = true; };
};
}
