rPackages: mark packages as broken when generating package sets

The current behaviour for generate-r-packages.R is to delete
packages that have been remove upstream. This patch changes the
behaviour to mark packages as broken rather than removing them.
This has the advantage of never breaking expressions, which
previously occured when a package with overrides in default.nix
was deleted. As a result, the update procedure is simplified,
allowing automated updates to the package tree to run, and
additionally if a package is re-established upstream the previous
overrides still exist.

doc/languages-frameworks/r.section.md

@@ -113,11 +113,3 @@ mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix
 ```
 
 `generate-r-packages.R <repo>` reads  `<repo>-packages.nix`, therefor the renaming.
-
-## Testing if the Nix-expression could be evaluated {#testing-if-the-nix-expression-could-be-evaluated}
-
-```bash
-nix-build test-evaluation.nix --dry-run
-```
-
-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)