118 lines
4.6 KiB
R
Executable file
118 lines
4.6 KiB
R
Executable file
#!/usr/bin/env Rscript
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# This script can be used to generate the .json file for a given R package set
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# that is part of the `rPackages` tree
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#
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# See R section of the nixpkgs manual for an example of how to use this script
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library(data.table)
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library(parallel)
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library(BiocManager)
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library(jsonlite)
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# always order strings according to POSIX ordering
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locale <- Sys.setlocale(locale = "C")
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biocVersion <- BiocManager:::.version_map()
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biocVersion <- biocVersion[biocVersion$R == getRversion()[, 1:2],c("Bioc", "BiocStatus")]
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if ("release" %in% biocVersion$BiocStatus) {
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biocVersion <- as.numeric(as.character(biocVersion[biocVersion$BiocStatus == "release", "Bioc"]))
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} else {
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biocVersion <- max(as.numeric(as.character(biocVersion$Bioc)))
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}
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mirrorUrls <- list( bioc=paste0("http://bioconductor.org/packages/", biocVersion, "/bioc/src/contrib/")
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, "bioc-annotation"=paste0("http://bioconductor.org/packages/", biocVersion, "/data/annotation/src/contrib/")
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, "bioc-experiment"=paste0("http://bioconductor.org/packages/", biocVersion, "/data/experiment/src/contrib/")
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, cran="https://cran.r-project.org/src/contrib/"
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)
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mirrorType <- commandArgs(trailingOnly=TRUE)[1]
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stopifnot(mirrorType %in% names(mirrorUrls))
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packagesFile <- paste(mirrorType, 'packages.json', sep='-')
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prevPkgs <- fromJSON(packagesFile)$packages
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write(paste("downloading package lists"), stderr())
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pkgTables <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates")), method="libcurl"))
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knownPackageNames <- c(unique(do.call("rbind", pkgTables)$Package))
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pkgTable <- pkgTables[mirrorType][[1]]
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mirrorUrl <- mirrorUrls[mirrorType][[1]]
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escapeName <- function(name) {
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gsub(".", "_", switch(name, "import" = "r_import", "assert" = "r_assert", name), fixed=TRUE)
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}
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nixPrefetch <- function(name, version) {
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prevPkg <- prevPkgs[[escapeName(name)]]
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if (!is.null(prevPkg) && prevPkg$version == version)
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prevPkg$sha256
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else {
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# avoid nix-prefetch-url because it often fails to fetch/hash large files
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url <- paste0(mirrorUrl, name, "_", version, ".tar.gz")
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tmp <- tempfile(pattern=paste0(name, "_", version), fileext=".tar.gz")
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cmd <- paste0("wget -q -O '", tmp, "' '", url, "'")
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if(mirrorType == "cran"){
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archiveUrl <- paste0(mirrorUrl, "Archive/", name, "/", name, "_", version, ".tar.gz")
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cmd <- paste0(cmd, " || wget -q -O '", tmp, "' '", archiveUrl, "'")
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}
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cmd <- paste0(cmd, " && nix-hash --type sha256 --base32 --flat '", tmp, "'")
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cmd <- paste0(cmd, " && echo >&2 ' added ", name, " v", version, "'")
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cmd <- paste0(cmd, " ; rm -rf '", tmp, "'")
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system(cmd, intern=TRUE)
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}
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}
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formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
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options(warn=5)
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depends <- paste( if (is.na(depends)) "" else gsub("[ \t\n]+", "", depends)
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, if (is.na(imports)) "" else gsub("[ \t\n]+", "", imports)
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, if (is.na(linkingTo)) "" else gsub("[ \t\n]+", "", linkingTo)
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, sep=","
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)
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depends <- unlist(strsplit(depends, split=",", fixed=TRUE))
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depends <- lapply(depends, gsub, pattern="([^ \t\n(]+).*", replacement="\\1")
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depends <- depends[depends %in% knownPackageNames]
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depends <- lapply(depends, escapeName)
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depends <- paste(depends)
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depends <- sort(unique(depends))
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list(name=unbox(name), version=unbox(version), sha256=unbox(sha256), depends=depends)
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}
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cl <- makeCluster(10)
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clusterExport(cl, c("escapeName", "nixPrefetch", "prevPkgs", "mirrorUrl", "mirrorType", "knownPackageNames"))
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write(paste("updating", mirrorType, "packages"), stderr())
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pkgTable$sha256 <- parApply(cl, pkgTable, 1, function(p) nixPrefetch(p[1], p[2]))
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stopCluster(cl)
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pkgs <- lapply(1:nrow(pkgTable), function(i) with(pkgTable[i,], formatPackage(Package, Version, sha256, Depends, Imports, LinkingTo)))
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names(pkgs) <- lapply(pkgs, function(p) escapeName(p$name))
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# Mark deleted packages as broken
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brokenPkgs <- lapply(prevPkgs[setdiff(names(prevPkgs), names(pkgs))], function(p)
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list(name=unbox(p$name),
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version=unbox(p$version),
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sha256=unbox(p$sha256),
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depends=p$depends,
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broken=unbox(T)))
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# sort packages by their non-escaped names
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pkgs <- pkgs[order(sapply(pkgs, function(p) p$name))]
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brokenPkgs<- brokenPkgs[order(sapply(brokenPkgs, function(p) p$name))]
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# empty named list
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extraArgs = setNames(list(), character(0))
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if (mirrorType != "cran") {
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extraArgs=list(biocVersion=unbox(paste(biocVersion)))
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}
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cat(toJSON(list(extraArgs=extraArgs, packages=c(pkgs, brokenPkgs)), pretty=TRUE))
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cat("\n")
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write("done", stderr())
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