[ESS] Launching R executables within custom shell environments
Dominic Steinitz
dom|n|c @end|ng |rom @te|n|tz@org
Tue Apr 5 16:30:44 CEST 2022
> Dear ESS users,
>
> I'm interested if there is anyone on this mailing list who uses Emacs
> Speaks Statistics from within Guix or Nix, both of which bake
> reproducibility directly into their operating systems) or from anyone
> who might otherwise be familiar with some elisp code which uses the ESS
> remote session functionality to start an R interpreter from a different
> environment on the local system (such that it behaves great without
> having to worry about conflicting environment variables)?
>
> That was a mouthful, but I hope that was enough to peak someones
> interest. I'm just looking to see if this problem has already been
> well handled.
>
> Thanks,
> Kyle
Hi Kyle,
I use `direnv` and https://github.com/purcell/envrc. I can’t remember the exact sequence but I think I did `nix-env -i direnv` and then set up a `.envrc` with the line `use nix` in it. You might have to do `M-x envrc-allow`. Then your nix environment is available in emacs (as well as the same one being in a shell). Then I just `M-x R`.
FWIW I have
```
'(package-selected-packages
'(forge poly-markdown polymode poly-R envrc direnv json-mode stan-mode git-timemachine ein markdown-mode exec-path-from-shell nix-mode ess matlab-mode haskell-mode helm magit use-package))
```
And my current `shell.nix` is
```
let
rOverlay = rself: rsuper: {
rPackages = rsuper.rPackages.override {
overrides = {
smcsamplers = (rself.rPackages.buildRPackage {
name = "smcsamplers";
src = rself.fetchFromGitHub {
owner = "pierrejacob";
repo = "smcsamplers";
rev = "097192f7d5df520d9b026d442dfec493a3051374";
sha256 = "00facn1ylcbai4sbcidpp991899csz2ppmmkv0khvqxfncddr0f2";
};
propagatedBuildInputs = [ rsuper.rPackages.coda rsuper.rPackages.MASS rsuper.rPackages.mvtnorm rsuper.rPackages.loo rsuper.rPackages.shape rsuper.rPackages.rstan rsuper.rPackages.tidyverse rsuper.rPackages.doParallel rsuper.rPackages.igraph rsuper.rPackages.ggraph rsuper.rPackages.doRNG rsuper.rPackages.reshape2 ];
});
cmdstanr = (rself.rPackages.buildRPackage {
name = "cmdstanr";
src = rself.fetchFromGitHub {
owner = "stan-dev";
repo = "cmdstanr";
rev = "2e24ec873c5513b41fba90ee59e0dffcd27a479c";
sha256 = "sha256:0nrqlidsrykszasdypsldsbhv4dcbrj9awyyzq7rb6kc5y8fnhvi";
};
propagatedBuildInputs = [ rsuper.rPackages.coda rsuper.rPackages.MASS rsuper.rPackages.mvtnorm rsuper.rPackages.loo rsuper.rPackages.shape rsuper.rPackages.rstan rsuper.rPackages.tidyverse rsuper.rPackages.doParallel rsuper.rPackages.igraph rsuper.rPackages.ggraph rsuper.rPackages.doRNG rsuper.rPackages.reshape2 rsuper.rPackages.data_table rsuper.rPackages.posterior ];
});
};
};
};
myHaskellPackageOverlay = self: super: {
myHaskellPackages = super.haskell.packages.ghc921.override {
overrides = hself: hsuper: rec {
inline-r = super.haskell.lib.dontCheck (
hself.callCabal2nixWithOptions "inline-r" (builtins.fetchGit {
url = "https://github.com/tweag/HaskellR";
rev = "c3ba1023480e26ade420896bcb629ceaad59f308";
}) "--subpath inline-r" { });
singletons = self.haskell.lib.addBuildDepends(
hself.callHackageDirect {
pkg = "singletons";
ver = "3.0.1";
sha256 = "sha256-ixHWZae6AxjRUldMgpYolXBGsOUT5ZVIw9HZkxrhHQ0=";
} { }) [ ];
};
};
};
in
{ nixpkgs ? import "/Users/dom/nixpkgs" {
config.allowBroken = true;
overlays = [ myHaskellPackageOverlay rOverlay ];
# system = "x86_64-darwin";
}
}:
let
R-with-my-packages = nixpkgs.rWrapper.override{
packages = with nixpkgs.rPackages; [
ggplot2
]; };
pkgs = nixpkgs;
haskellDeps = ps: with ps; [
base
cassava
conduit
Frames
streamly
(pkgs.haskell.lib.dontCheck Frames-streamly)
hasql
http-client
http-client-tls
http-conduit
postgresql-binary
(pkgs.haskell.lib.dontCheck inline-r)
resourcet
time
vinyl
xlsx
zip
];
in
pkgs.stdenv.mkDerivation {
name = "xxx";
buildInputs = with pkgs.rPackages; [
pkgs.libintlOrEmpty
R-with-my-packages
(pkgs.myHaskellPackages.ghcWithPackages haskellDeps)
pkgs.darwin.apple_sdk.frameworks.Cocoa
];
shellHook = ''
R_LIBS_USER=$(Rscript -e ".libPaths()" | cut -c 6- | sed 's/[ \t]*$//' | sed 's/"//g' | sed -z 's/\n/:/g;s/:'''$/\n/' | sed 's/ //g')
export R_LIBS_USER
'';
}
```
I am guessing you don’t need the Haskell stuff. `The shellHook` is there so that Haskell picks up the “right” set of R libraries. I am sure it can be improved; I am barely an intermediate nix user. Oh I nearly forgot - because I was trying to fix something, I am pointing at my local copy of Nixpkgs. Clearly it should be pinned to something more permanent and reproducible.
Dominic Steinitz
dominic using steinitz.org
http://idontgetoutmuch.org
Twitter: @idontgetoutmuch
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