r-modules: use HTTPS, allow passing args from generated set, use MRAN

1 files changed, 17 insertions, 9 deletions

diff --git a/pkgs/development/r-modules/generate-r-packages.R b/pkgs/development/r-modules/generate-r-packages.R
index 4c5654184509..d45401b957de 100755
--- a/pkgs/development/r-modules/generate-r-packages.R
+++ b/pkgs/development/r-modules/generate-r-packages.R
@@ -7,14 +7,16 @@ mirrorType <- commandArgs(trailingOnly=TRUE)[1]
 stopifnot(mirrorType %in% c("bioc","cran", "irkernel"))
 
 packagesFile <- paste(mirrorType, 'packages.nix', sep='-')
-readFormatted <- as.data.table(read.table(skip=6, sep='"', text=head(readLines(packagesFile), -1)))
+readFormatted <- as.data.table(read.table(skip=8, sep='"', text=head(readLines(packagesFile), -1)))
+rVersion <- paste(R.Version()$major, strsplit(R.Version()$minor, ".", fixed=TRUE)[[1]][1], sep=".")
+snapshotDate <- Sys.Date()
 
-mirrorUrls <- list( bioc="http://bioconductor.statistik.tu-dortmund.de/packages/3.2/bioc/src/contrib/"
-                  , cran="http://cran.r-project.org/src/contrib/"
-                  , irkernel="http://irkernel.github.io/src/contrib/"
+mirrorUrls <- list( bioc=paste0("https://bioconductor.statistik.tu-dortmund.de/packages/", rVersion, "/bioc/src/contrib/")
+                  , cran=paste0("https://mran.revolutionanalytics.com/snapshot/", snapshotDate, "/src/contrib/")
+                  , irkernel="https://irkernel.github.io/src/contrib/"
                   )
 mirrorUrl <- mirrorUrls[mirrorType][[1]]
-knownPackages <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates"))))
+knownPackages <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates")), method="libcurl"))
 pkgs <- knownPackages[mirrorType][[1]]
 setkey(pkgs, Package)
 knownPackages <- c(unique(do.call("rbind", knownPackages)$Package))
@@ -38,12 +40,12 @@ formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
     depends <- sapply(depends, gsub, pattern=".", replacement="_", fixed=TRUE)
     depends <- depends[depends %in% knownPackages]
     depends <- paste(sort(unique(depends)), collapse=" ")
-    paste0(attr, " = derive { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
+    paste0("  ", attr, " = derive2 { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
 }
 
 clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "knownPackages"))
 
-pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates")))
+pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates"), method="libcurl"))
 pkgs <- pkgs[order(Package)]
 pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))
 
@@ -54,8 +56,14 @@ cat("# Execute the following command to update the file.\n")
 cat("#\n")
 cat(paste("# Rscript generate-r-packages.R", mirrorType, ">new && mv new", packagesFile))
 cat("\n\n")
-cat("{ self, derive }: with self; {\n")
-cat(paste(nix, collapse="\n"), "\n")
+cat("{ self, derive }:\n")
+cat("let derive2 = derive ")
+if (mirrorType == "bioc") { cat("{ rVersion = \"", rVersion, "\"; }", sep="")
+} else if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
+} else if (mirrorType == "irkernel") { cat("{}") }
+cat(";\n")
+cat("in with self; {\n")
+cat(paste(nix, collapse="\n"), "\n", sep="")
 cat("}\n")
 
 stopCluster(cl)