RStudio: Optionally allow packages from custom R environment

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; };
  };
}

pkgs/applications/editors/rstudio/default.nix

@@ -1,4 +1,14 @@
-{ stdenv, fetchurl, makeDesktopItem, cmake, boost155, zlib, openssl, R, qt4, libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper }:
+{ stdenv, fetchurl, makeDesktopItem, cmake, boost155, zlib, openssl,
+R, qt4, libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper,
+# If you have set up an R wrapper with other packages by following
+# something like https://nixos.org/nixpkgs/manual/#r-packages, RStudio
+# by default not be able to access any of those R packages. In order
+# to do this, override the argument "R" here with your respective R
+# wrapper, and set "useRPackages" to true.  This will add the
+# environment variable R_PROFILE_USER to the RStudio wrapper, pointing
+# to an R script which will allow R to use these packages.
+useRPackages ? false
+}:
 
 let
   version = "0.98.110";
@@ -72,8 +82,14 @@ stdenv.mkDerivation rec {
     mimeType = "text/x-r-source;text/x-r;text/x-R;text/x-r-doc;text/x-r-sweave;text/x-r-markdown;text/x-r-html;text/x-r-presentation;application/x-r-data;application/x-r-project;text/x-r-history;text/x-r-profile;text/x-tex;text/x-markdown;text/html;text/css;text/javascript;text/x-chdr;text/x-csrc;text/x-c++hdr;text/x-c++src;";
   };
 
-  postInstall = ''
-      wrapProgram $out/bin/rstudio --suffix PATH : ${gnumake}/bin
+  postInstall = let rProfile =
+    # RStudio seems to bypass the environment variables that the R
+    # wrapper already applies, and so this sets R_PROFILE_USER to
+    # again make those R packages accessible:
+    if useRPackages
+    then "--set R_PROFILE_USER ${R}/${R.passthru.fixLibsR}" else "";
+    in ''
+      wrapProgram $out/bin/rstudio --suffix PATH : ${gnumake}/bin ${rProfile}
       mkdir $out/share
       cp -r ${desktopItem}/share/applications $out/share
       mkdir $out/share/icons

pkgs/development/r-modules/README.md

@@ -53,6 +53,37 @@ in with pkgs; {
 and then run `nix-shell .` to be dropped into a shell with those packages
 available.
 
+## RStudio
+
+RStudio by default will not use the libraries installed like above.
+You must override its R version with your custom R environment, and
+set `useRPackages` to `true`, like below:
+
+```nix
+{
+    packageOverrides = super: let self = super.pkgs; in
+    {
+
+        rEnv = super.rWrapper.override {
+            packages = with self.rPackages; [ 
+                devtools
+                ggplot2
+                reshape2
+                yaml
+                optparse
+                ];
+        };
+        rstudioEnv = super.rstudio.override {
+            R = rEnv;
+            useRPackages = true;
+        };
+    };
+}
+```
+
+Then like above, `nix-env -f "<nixpkgs>" -iA rstudioEnv` will install
+this into your user profile.
+
 ## Updating the package set
 
 ```bash

pkgs/development/r-modules/wrapper.nix

@@ -1,12 +1,19 @@
 { stdenv, R, makeWrapper, recommendedPackages, packages }:
 
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
   name = R.name + "-wrapper";
 
   buildInputs = [makeWrapper R] ++ recommendedPackages ++ packages;
 
   unpackPhase = ":";
 
+  # This filename is used in 'installPhase', but needs to be
+  # referenced elsewhere.  This will be relative to this package's
+  # path.
+  passthru = {
+    fixLibsR = "fix_libs.R";
+  };
+  
   installPhase = ''
     mkdir -p $out/bin
     cd ${R}/bin
@@ -14,6 +21,17 @@ stdenv.mkDerivation {
       makeWrapper ${R}/bin/$exe $out/bin/$exe \
         --prefix "R_LIBS_SITE" ":" "$R_LIBS_SITE"
     done
+    # RStudio (and perhaps other packages) overrides the R_LIBS_SITE
+    # which the wrapper above applies, and as a result packages
+    # installed in the wrapper (as in the method described in
+    # https://nixos.org/nixpkgs/manual/#r-packages) aren't visible.
+    # The below turns R_LIBS_SITE into some R startup code which can
+    # correct this.
+    echo "# Autogenerated by wrapper.nix from R_LIBS_SITE" > $out/${passthru.fixLibsR}
+    echo -n ".libPaths(c(.libPaths(), \"" >> $out/${passthru.fixLibsR}
+    echo -n $R_LIBS_SITE | sed -e 's/:/", "/g' >> $out/${passthru.fixLibsR}
+    echo -n "\"))" >> $out/${passthru.fixLibsR}
+    echo >> $out/${passthru.fixLibsR}
   '';
 
   meta = {