diff options
Diffstat (limited to 'doc/languages-frameworks/r.section.md')
-rw-r--r-- | doc/languages-frameworks/r.section.md | 27 |
1 files changed, 15 insertions, 12 deletions
diff --git a/doc/languages-frameworks/r.section.md b/doc/languages-frameworks/r.section.md index d4e1617779c..56e3da64df2 100644 --- a/doc/languages-frameworks/r.section.md +++ b/doc/languages-frameworks/r.section.md @@ -1,7 +1,6 @@ -R -= +# R {#r} -## Installation +## 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: @@ -32,15 +31,14 @@ 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 -let - pkgs = import <nixpkgs> {}; - stdenv = pkgs.stdenv; -in with pkgs; { +with import <nixpkgs> {}; +{ myProject = stdenv.mkDerivation { name = "myProject"; version = "1"; - src = if pkgs.lib.inNixShell then null else nix; + src = if lib.inNixShell then null else nix; buildInputs = with rPackages; [ R @@ -53,7 +51,7 @@ in with pkgs; { and then run `nix-shell .` to be dropped into a shell with those packages available. -## RStudio +## 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 @@ -96,7 +94,7 @@ 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 {#updating-the-package-set} ```bash nix-shell generate-shell.nix @@ -106,12 +104,17 @@ 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`, therefor the renaming. - -## Testing if the Nix-expression could be evaluated +## Testing if the Nix-expression could be evaluated {#testing-if-the-nix-expression-could-be-evaluated} ```bash nix-build test-evaluation.nix --dry-run |