From 287f99badae394c38a200170a60189d74d1f52f9 Mon Sep 17 00:00:00 2001 From: Nikolay Amiantov Date: Tue, 24 Nov 2015 16:59:04 +0300 Subject: r-modules: use HTTPS, allow passing args from generated set, use MRAN --- pkgs/development/r-modules/generate-r-packages.R | 26 ++++++++++++++++-------- 1 file changed, 17 insertions(+), 9 deletions(-) (limited to 'pkgs/development/r-modules/generate-r-packages.R') diff --git a/pkgs/development/r-modules/generate-r-packages.R b/pkgs/development/r-modules/generate-r-packages.R index 4c56541845099..d45401b957de9 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) -- cgit 1.4.1