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

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Nikolay Amiantov
2015-11-25 11:39:28 +01:00
committed by Peter Simons
parent 5ee5b5ba82
commit 287f99bada
4 changed files with 53 additions and 134 deletions
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pkgs/development/r-modules/generate-r-packages.R
+17 -9
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@@ -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)