mirror of
https://github.com/NixOS/nixpkgs.git
synced 2024-12-22 21:53:32 +00:00
9bc37bff1a
The current behaviour for generate-r-packages.R is to delete packages that have been remove upstream. This patch changes the behaviour to mark packages as broken rather than removing them. This has the advantage of never breaking expressions, which previously occured when a package with overrides in default.nix was deleted. As a result, the update procedure is simplified, allowing automated updates to the package tree to run, and additionally if a package is re-established upstream the previous overrides still exist.
113 lines
5.0 KiB
R
Executable File
113 lines
5.0 KiB
R
Executable File
#!/usr/bin/env Rscript
|
|
library(data.table)
|
|
library(parallel)
|
|
library(BiocManager)
|
|
cl <- makeCluster(10)
|
|
|
|
biocVersion <- BiocManager:::.version_map()
|
|
biocVersion <- biocVersion[biocVersion$R == getRversion()[, 1:2],c("Bioc", "BiocStatus")]
|
|
if ("release" %in% biocVersion$BiocStatus) {
|
|
biocVersion <- as.numeric(as.character(biocVersion[biocVersion$BiocStatus == "release", "Bioc"]))
|
|
} else {
|
|
biocVersion <- max(as.numeric(as.character(biocVersion$Bioc)))
|
|
}
|
|
snapshotDate <- Sys.Date()-1
|
|
|
|
mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/bioc/src/contrib/")
|
|
, "bioc-annotation"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/annotation/src/contrib/")
|
|
, "bioc-experiment"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/experiment/src/contrib/")
|
|
, cran=paste0("http://mran.revolutionanalytics.com/snapshot/", snapshotDate, "/src/contrib/")
|
|
)
|
|
|
|
mirrorType <- commandArgs(trailingOnly=TRUE)[1]
|
|
stopifnot(mirrorType %in% names(mirrorUrls))
|
|
packagesFile <- paste(mirrorType, 'packages.nix', sep='-')
|
|
readFormatted <- as.data.table(read.table(skip=8, sep='"', text=head(readLines(packagesFile), -1)))
|
|
|
|
write(paste("downloading package lists"), stderr())
|
|
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)$Package))
|
|
knownPackages <- sapply(knownPackages, gsub, pattern=".", replacement="_", fixed=TRUE)
|
|
|
|
mirrorUrl <- mirrorUrls[mirrorType][[1]]
|
|
nixPrefetch <- function(name, version) {
|
|
prevV <- readFormatted$V2 == name & readFormatted$V4 == version
|
|
if (sum(prevV) == 1)
|
|
as.character(readFormatted$V6[ prevV ])
|
|
|
|
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, "'")
|
|
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)
|
|
}
|
|
|
|
}
|
|
|
|
escapeName <- function(name) {
|
|
switch(name, "import" = "r_import", "assert" = "r_assert", name)
|
|
}
|
|
|
|
formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
|
|
attr <- gsub(".", "_", escapeName(name), fixed=TRUE)
|
|
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 <- lapply(depends, gsub, pattern=".", replacement="_", fixed=TRUE)
|
|
depends <- depends[depends %in% knownPackages]
|
|
depends <- lapply(depends, escapeName)
|
|
depends <- paste(depends)
|
|
depends <- paste(sort(unique(depends)), collapse=" ")
|
|
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"), method="libcurl"))
|
|
pkgs <- pkgs[order(Package)]
|
|
|
|
write(paste("updating", mirrorType, "packages"), stderr())
|
|
pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))
|
|
nix <- apply(pkgs, 1, function(p) formatPackage(p[1], p[2], p[18], p[4], p[5], p[6]))
|
|
write("done", stderr())
|
|
|
|
# Mark deleted packages as broken
|
|
setkey(readFormatted, V2)
|
|
markBroken <- function(name) {
|
|
str <- paste0(readFormatted[name], collapse='"')
|
|
if(sum(grep("broken = true;", str)))
|
|
return(str)
|
|
write(paste("marked", name, "as broken"), stderr())
|
|
gsub("};$", "broken = true; };", str)
|
|
}
|
|
broken <- lapply(setdiff(readFormatted[[2]], pkgs[[1]]), markBroken)
|
|
|
|
cat("# This file is generated from generate-r-packages.R. DO NOT EDIT.\n")
|
|
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 }:\n")
|
|
cat("let derive2 = derive ")
|
|
if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
|
|
} else if (mirrorType == "irkernel") { cat("{}")
|
|
} else { cat("{ biocVersion = \"", biocVersion, "\"; }", sep="") }
|
|
cat(";\n")
|
|
cat("in with self; {\n")
|
|
cat(paste(nix, collapse="\n"), "\n", sep="")
|
|
cat(paste(broken, collapse="\n"), "\n", sep="")
|
|
cat("}\n")
|
|
|
|
stopCluster(cl)
|