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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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doc/languages-frameworks/r.section.md
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@ -104,24 +104,27 @@ directory and executed as follows:
```bash ```bash
nix-shell generate-shell.nix nix-shell generate-shell.nix
Rscript generate-r-packages.R cran > cran-packages.nix.new Rscript generate-r-packages.R cran > cran-packages.json.new
mv cran-packages.nix.new cran-packages.nix mv cran-packages.json.new cran-packages.json
Rscript generate-r-packages.R bioc > bioc-packages.nix.new Rscript generate-r-packages.R bioc > bioc-packages.json.new
mv bioc-packages.nix.new bioc-packages.nix mv bioc-packages.json.new bioc-packages.json
Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.nix.new Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.json.new
mv bioc-annotation-packages.nix.new bioc-annotation-packages.nix mv bioc-annotation-packages.json.new bioc-annotation-packages.json
Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.nix.new Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.json.new
mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix 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 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 Some packages require overrides to specify external dependencies or other
patches and special requirements. These overrides are specified in the 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 contents are automatically generated it should not be edited and broken
builds should be addressed using overrides. builds should be addressed using overrides.