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doc: update R section to mention .json files

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TomaSajt 2024-07-24 13:07:30 +02:00
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23
doc/languages-frameworks/r.section.md
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@ -104,24 +104,27 @@ 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 cran > cran-packages.json.new
mv cran-packages.json.new cran-packages.json
Rscript generate-r-packages.R bioc > bioc-packages.nix.new
mv bioc-packages.nix.new bioc-packages.nix
Rscript generate-r-packages.R bioc > bioc-packages.json.new
mv bioc-packages.json.new bioc-packages.json
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-annotation > bioc-annotation-packages.json.new
mv bioc-annotation-packages.json.new bioc-annotation-packages.json
Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.nix.new
mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix
Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.json.new
mv bioc-experiment-packages.json.new bioc-experiment-packages.json
```
`generate-r-packages.R <repo>` reads `<repo>-packages.nix`, therefore
`generate-r-packages.R <repo>` reads `<repo>-packages.json`, therefore
the renaming.
The contents of a generated `*-packages.json` file will be used to
create a package derivation for each R package listed in the file.
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`
`pkgs/development/r-modules/default.nix` file. As the `*-packages.json`
contents are automatically generated it should not be edited and broken
builds should be addressed using overrides.