pyrox.dev
Merge pull request #139312 from jbedo/r-broken
rPackages: mark packages as broken when generating package sets
authored by Matthieu Coudron and committed by GitHub 639df4e2 92357f5e
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doc/languages-frameworks/r.section.md
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doc/languages-frameworks/r.section.md
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## Updating the package set {#updating-the-package-set}
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```bash
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nix-shell generate-shell.nix
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mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix
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```
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`generate-r-packages.R <repo>` reads `<repo>-packages.nix`, therefor the renaming.
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## Testing if the Nix-expression could be evaluated {#testing-if-the-nix-expression-could-be-evaluated}
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```bash
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nix-build test-evaluation.nix --dry-run
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```
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If this exits fine, the expression is ok. If not, you have to edit `default.nix`
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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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mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix
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```
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`generate-r-packages.R <repo>` reads `<repo>-packages.nix`, therefore
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the renaming.
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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.nix`
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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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pkgs/development/r-modules/generate-r-packages.R
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pkgs/development/r-modules/generate-r-packages.R
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nix <- apply(pkgs, 1, function(p) formatPackage(p[1], p[2], p[18], p[4], p[5], p[6]))
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write("done", stderr())
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cat("# This file is generated from generate-r-packages.R. DO NOT EDIT.\n")
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cat("# Execute the following command to update the file.\n")
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cat("#\n")
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cat(";\n")
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cat("in with self; {\n")
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cat(paste(nix, collapse="\n"), "\n", sep="")
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cat("}\n")
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stopCluster(cl)
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nix <- apply(pkgs, 1, function(p) formatPackage(p[1], p[2], p[18], p[4], p[5], p[6]))
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write("done", stderr())
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# Mark deleted packages as broken
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setkey(readFormatted, V2)
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markBroken <- function(name) {
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str <- paste0(readFormatted[name], collapse='"')
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if(sum(grep("broken = true;", str)))
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return(str)
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write(paste("marked", name, "as broken"), stderr())
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gsub("};$", "broken = true; };", str)
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}
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broken <- lapply(setdiff(readFormatted[[2]], pkgs[[1]]), markBroken)
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cat("# This file is generated from generate-r-packages.R. DO NOT EDIT.\n")
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cat("# Execute the following command to update the file.\n")
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cat("#\n")
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cat(";\n")
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cat("in with self; {\n")
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cat(paste(nix, collapse="\n"), "\n", sep="")
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cat(paste(broken, collapse="\n"), "\n", sep="")
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cat("}\n")
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stopCluster(cl)