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