Merge pull request #139312 from jbedo/r-broken

rPackages: mark packages as broken when generating package sets

doc/languages-frameworks/r.section.md

@@ -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
 
@@ -112,12 +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.
 
-## Testing if the Nix-expression could be evaluated {#testing-if-the-nix-expression-could-be-evaluated}
+Some packages require overrides to specify external dependencies or other
-
+patches and special requirements. These overrides are specified in the
-```bash
+`pkgs/development/r-modules/default.nix` file. As the `*-packages.nix`
-nix-build test-evaluation.nix --dry-run
+contents are automatically generated it should not be edited and broken
-```
+builds should be addressed using overrides.
-
-If this exits fine, the expression is ok. If not, you have to edit `default.nix`

pkgs/development/r-modules/generate-r-packages.R

@@ -82,6 +82,17 @@ pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))
 nix <- apply(pkgs, 1, function(p) formatPackage(p[1], p[2], p[18], p[4], p[5], p[6]))
 write("done", stderr())
 
+# Mark deleted packages as broken
+setkey(readFormatted, V2)
+markBroken <- function(name) {
+  str <- paste0(readFormatted[name], collapse='"')
+  if(sum(grep("broken = true;", str)))
+    return(str)
+  write(paste("marked", name, "as broken"), stderr())
+  gsub("};$", "broken = true; };", str)
+}
+broken <- lapply(setdiff(readFormatted[[2]], pkgs[[1]]), markBroken)
+
 cat("# This file is generated from generate-r-packages.R. DO NOT EDIT.\n")
 cat("# Execute the following command to update the file.\n")
 cat("#\n")
@@ -95,6 +106,7 @@ if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }",
 cat(";\n")
 cat("in with self; {\n")
 cat(paste(nix, collapse="\n"), "\n", sep="")
+cat(paste(broken, collapse="\n"), "\n", sep="")
 cat("}\n")
 
 stopCluster(cl)