R: add support for Bioconductor packages

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

@@ -0,0 +1,54 @@
+#!/usr/bin/env Rscript
+
+library(data.table)
+library(parallel)
+cl <- makeCluster(10)
+
+mirrorType <- commandArgs(trailingOnly=TRUE)[1]
+packagesFile <- paste(mirrorType, 'packages.nix', sep='-')
+mirrorUrls <- list(
+  bioc="http://bioconductor.statistik.tu-dortmund.de/packages/3.0/bioc",
+  cran="http://cran.r-project.org"
+)
+mirrorUrl <- paste(mirrorUrls[mirrorType], "/src/contrib/", sep="")
+
+readFormatted <- as.data.table(read.table(skip=6, sep='"', text=head(readLines(packagesFile), -1)))
+
+nixPrefetch <- function(name, version) {
+  prevV <- readFormatted$V2 == name & readFormatted$V4 == version
+  if (sum(prevV) == 1) as.character(readFormatted$V6[ prevV ]) else
+    system(paste0("nix-prefetch-url --type sha256 ", mirrorUrl, name, "_", version, ".tar.gz"), intern=TRUE)
+}
+
+formatPackage <- function(name, version, sha256, depends, imports, linkingTo, knownPackages) {
+    attr <- gsub(".", "_", name, fixed=TRUE)
+    if (is.na(depends)) depends <- "";
+    depends <- unlist(strsplit(depends, split="[ \t\n]*,[ \t\n]*", fixed=FALSE))
+    depends <- c(depends, unlist(strsplit(imports, split="[ \t\n]*,[ \t\n]*", fixed=FALSE)))
+    depends <- c(depends, unlist(strsplit(linkingTo, split="[ \t\n]*,[ \t\n]*", fixed=FALSE)))
+    depends <- sapply(depends, gsub, pattern="([^ \t\n(]+).*", replacement="\\1")
+    depends <- depends[depends %in% knownPackages]
+    depends <- sapply(depends, gsub, pattern=".", replacement="_", fixed=TRUE)
+    depends <- paste(depends, collapse=" ")
+    paste0(attr, " = derive { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
+}
+
+clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl"))
+
+pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates")))
+pkgs <- pkgs[order(Package)]
+pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))
+knownPackages <- unique(pkgs$Package)
+
+nix <- apply(pkgs, 1, function(p) formatPackage(p[1], p[2], p[18], p[4], p[5], p[6], knownPackages))
+
+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")
+cat(paste("# Rscript generate-r-packages.R", mirrorType, ">", packagesFile))
+cat("\n\n")
+cat("{ self, derive }: with self; {\n")
+cat(paste(nix, collapse="\n"), "\n")
+cat("}\n")
+
+stopCluster(cl)