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What happens if I push all of nixpkgs
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R
123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118#!/usr/bin/env Rscript
# This script can be used to generate the .json file for a given R package set# that is part of the `rPackages` tree## See R section of the nixpkgs manual for an example of how to use this script
library(data.table)library(parallel)library(BiocManager)library(jsonlite)
# always order strings according to POSIX orderinglocale <- Sys.setlocale(locale = "C")
biocVersion <- BiocManager:::.version_map()biocVersion <- biocVersion[biocVersion$R == getRversion()[, 1:2],c("Bioc", "BiocStatus")]if ("release" %in% biocVersion$BiocStatus) { biocVersion <- as.character(biocVersion[biocVersion$BiocStatus == "release", "Bioc"])} else { biocVersion <- max(as.character(biocVersion$Bioc))}
mirrorUrls <- list( bioc=paste0("http://bioconductor.org/packages/", biocVersion, "/bioc/src/contrib/") , "bioc-annotation"=paste0("http://bioconductor.org/packages/", biocVersion, "/data/annotation/src/contrib/") , "bioc-experiment"=paste0("http://bioconductor.org/packages/", biocVersion, "/data/experiment/src/contrib/") , cran="https://cran.r-project.org/src/contrib/" )
mirrorType <- commandArgs(trailingOnly=TRUE)[1]stopifnot(mirrorType %in% names(mirrorUrls))
packagesFile <- paste(mirrorType, 'packages.json', sep='-')prevPkgs <- fromJSON(packagesFile)$packages
write(paste("downloading package lists"), stderr())pkgTables <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates")), method="libcurl"))knownPackageNames <- c(unique(do.call("rbind", pkgTables)$Package))
pkgTable <- pkgTables[mirrorType][[1]]mirrorUrl <- mirrorUrls[mirrorType][[1]]
escapeName <- function(name) { gsub(".", "_", switch(name, "import" = "r_import", "assert" = "r_assert", name), fixed=TRUE)}
nixPrefetch <- function(name, version) { prevPkg <- prevPkgs[[escapeName(name)]] if (!is.null(prevPkg) && prevPkg$version == version) prevPkg$sha256
else { # avoid nix-prefetch-url because it often fails to fetch/hash large files url <- paste0(mirrorUrl, name, "_", version, ".tar.gz") tmp <- tempfile(pattern=paste0(name, "_", version), fileext=".tar.gz") cmd <- paste0("wget -q -O '", tmp, "' '", url, "'") if(mirrorType == "cran"){ archiveUrl <- paste0(mirrorUrl, "Archive/", name, "/", name, "_", version, ".tar.gz") cmd <- paste0(cmd, " || wget -q -O '", tmp, "' '", archiveUrl, "'") } cmd <- paste0(cmd, " && nix-hash --type sha256 --base32 --flat '", tmp, "'") cmd <- paste0(cmd, " && echo >&2 ' added ", name, " v", version, "'") cmd <- paste0(cmd, " ; rm -rf '", tmp, "'") system(cmd, intern=TRUE) }
}
formatPackage <- function(name, version, sha256, depends, imports, linkingTo) { options(warn=5) depends <- paste( if (is.na(depends)) "" else gsub("[ \t\n]+", "", depends) , if (is.na(imports)) "" else gsub("[ \t\n]+", "", imports) , if (is.na(linkingTo)) "" else gsub("[ \t\n]+", "", linkingTo) , sep="," ) depends <- unlist(strsplit(depends, split=",", fixed=TRUE)) depends <- lapply(depends, gsub, pattern="([^ \t\n(]+).*", replacement="\\1") depends <- depends[depends %in% knownPackageNames] depends <- lapply(depends, escapeName) depends <- paste(depends) depends <- sort(unique(depends)) list(name=unbox(name), version=unbox(version), sha256=unbox(sha256), depends=depends)}
cl <- makeCluster(10)clusterExport(cl, c("escapeName", "nixPrefetch", "prevPkgs", "mirrorUrl", "mirrorType", "knownPackageNames"))
write(paste("updating", mirrorType, "packages"), stderr())pkgTable$sha256 <- parApply(cl, pkgTable, 1, function(p) nixPrefetch(p[1], p[2]))
stopCluster(cl)
pkgs <- lapply(1:nrow(pkgTable), function(i) with(pkgTable[i,], formatPackage(Package, Version, sha256, Depends, Imports, LinkingTo)))names(pkgs) <- lapply(pkgs, function(p) escapeName(p$name))
# Mark deleted packages as brokenbrokenPkgs <- lapply(prevPkgs[setdiff(names(prevPkgs), names(pkgs))], function(p) list(name=unbox(p$name), version=unbox(p$version), sha256=unbox(p$sha256), depends=p$depends, broken=unbox(T)))
# sort packages by their non-escaped namespkgs <- pkgs[order(sapply(pkgs, function(p) p$name))]brokenPkgs<- brokenPkgs[order(sapply(brokenPkgs, function(p) p$name))]
# empty named listextraArgs = setNames(list(), character(0))
if (mirrorType != "cran") { extraArgs=list(biocVersion=unbox(paste(biocVersion)))}
cat(toJSON(list(extraArgs=extraArgs, packages=c(pkgs, brokenPkgs)), pretty=TRUE))cat("\n")write("done", stderr())