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doc: clarify location of rPackages overrides

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Detail the location of rPackage overrides and how broken
builds should be addressed.
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Justin Bedo 2021-09-26 07:29:58 +10:00
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14
doc/languages-frameworks/r.section.md
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@ -96,6 +96,11 @@ 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
@ -112,4 +117,11 @@ 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.
`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.