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nixpkgs/pkgs/development/r-modules/generate-r-packages.R
Justin Bedo 9bc37bff1a
rPackages: mark packages as broken when generating package sets
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.
2021-09-24 21:25:53 +10:00

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R
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#!/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)