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+# R {#r}
+
+## Installation {#installation}
+
+Define an environment for R that contains all the libraries that you'd like to
+use by adding the following snippet to your $HOME/.config/nixpkgs/config.nix file:
+
+```nix
+{
+    packageOverrides = super: let self = super.pkgs; in
+    {
+
+        rEnv = super.rWrapper.override {
+            packages = with self.rPackages; [
+                devtools
+                ggplot2
+                reshape2
+                yaml
+                optparse
+                ];
+        };
+    };
+}
+```
+
+Then you can use `nix-env -f "<nixpkgs>" -iA rEnv` to install it into your user
+profile. The set of available libraries can be discovered by running the
+command `nix-env -f "<nixpkgs>" -qaP -A rPackages`. The first column from that
+output is the name that has to be passed to rWrapper in the code snipped above.
+
+However, if you'd like to add a file to your project source to make the
+environment available for other contributors, you can create a `default.nix`
+file like so:
+
+```nix
+with import <nixpkgs> {};
+{
+  myProject = stdenv.mkDerivation {
+    name = "myProject";
+    version = "1";
+    src = if lib.inNixShell then null else nix;
+
+    buildInputs = with rPackages; [
+      R
+      ggplot2
+      knitr
+    ];
+  };
+}
+```
+and then run `nix-shell .` to be dropped into a shell with those packages
+available.
+
+## RStudio {#rstudio}
+
+RStudio uses a standard set of packages and ignores any custom R
+environments or installed packages you may have.  To create a custom
+environment, see `rstudioWrapper`, which functions similarly to
+`rWrapper`:
+
+```nix
+{
+    packageOverrides = super: let self = super.pkgs; in
+    {
+
+        rstudioEnv = super.rstudioWrapper.override {
+            packages = with self.rPackages; [
+                dplyr
+                ggplot2
+                reshape2
+                ];
+        };
+    };
+}
+```
+
+Then like above, `nix-env -f "<nixpkgs>" -iA rstudioEnv` will install
+this into your user profile.
+
+Alternatively, you can create a self-contained `shell.nix` without the need to
+modify any configuration files:
+
+```nix
+{ pkgs ? import <nixpkgs> {}
+}:
+
+pkgs.rstudioWrapper.override {
+  packages = with pkgs.rPackages; [ dplyr ggplot2 reshape2 ];
+}
+
+```
+
+Executing `nix-shell` will then drop you into an environment equivalent to the
+one above. If you need additional packages just add them to the list and
+re-enter the shell.
+
+## Updating the package set {#updating-the-package-set}
+
+There is a script and associated environment for regenerating the package
+sets and synchronising the rPackages tree to the current CRAN and matching
+BIOC release. These scripts are found in the `pkgs/development/r-modules`
+directory and executed as follows:
+
+```bash
+nix-shell generate-shell.nix
+
+Rscript generate-r-packages.R cran  > cran-packages.nix.new
+mv cran-packages.nix.new cran-packages.nix
+
+Rscript generate-r-packages.R bioc  > bioc-packages.nix.new
+mv bioc-packages.nix.new bioc-packages.nix
+
+Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.nix.new
+mv bioc-annotation-packages.nix.new bioc-annotation-packages.nix
+
+Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.nix.new
+mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix
+```
+
+`generate-r-packages.R <repo>` reads  `<repo>-packages.nix`, therefore
+the renaming.
+
+Some packages require overrides to specify external dependencies or other
+patches and special requirements. These overrides are specified in the
+`pkgs/development/r-modules/default.nix` file. As the `*-packages.nix`
+contents are automatically generated it should not be edited and broken
+builds should be addressed using overrides.