tjh.dev
nixpkgs mirror (for testing)
github.com/NixOS/nixpkgs
nix
1#!/usr/bin/env Rscript
2library(data.table)
3library(parallel)
4library(BiocManager)
5cl <- makeCluster(10)
6
7biocVersion <- BiocManager:::.version_map()
8biocVersion <- biocVersion[biocVersion$R == getRversion()[, 1:2],c("Bioc", "BiocStatus")]
9if ("release" %in% biocVersion$BiocStatus) {
10 biocVersion <- as.numeric(as.character(biocVersion[biocVersion$BiocStatus == "release", "Bioc"]))
11} else {
12 biocVersion <- max(as.numeric(as.character(biocVersion$Bioc)))
13}
14snapshotDate <- Sys.Date()-1
15
16mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/bioc/src/contrib/")
17 , "bioc-annotation"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/annotation/src/contrib/")
18 , "bioc-experiment"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/experiment/src/contrib/")
19 , cran=paste0("http://mran.revolutionanalytics.com/snapshot/", snapshotDate, "/src/contrib/")
20 )
21
22mirrorType <- commandArgs(trailingOnly=TRUE)[1]
23stopifnot(mirrorType %in% names(mirrorUrls))
24packagesFile <- paste(mirrorType, 'packages.nix', sep='-')
25readFormatted <- as.data.table(read.table(skip=8, sep='"', text=head(readLines(packagesFile), -1)))
26
27write(paste("downloading package lists"), stderr())
28knownPackages <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates")), method="libcurl"))
29pkgs <- knownPackages[mirrorType][[1]]
30setkey(pkgs, Package)
31knownPackages <- c(unique(do.call("rbind", knownPackages)$Package))
32knownPackages <- sapply(knownPackages, gsub, pattern=".", replacement="_", fixed=TRUE)
33
34mirrorUrl <- mirrorUrls[mirrorType][[1]]
35nixPrefetch <- function(name, version) {
36 prevV <- readFormatted$V2 == name & readFormatted$V4 == version
37 if (sum(prevV) == 1)
38 as.character(readFormatted$V6[ prevV ])
39
40 else {
41 # avoid nix-prefetch-url because it often fails to fetch/hash large files
42 url <- paste0(mirrorUrl, name, "_", version, ".tar.gz")
43 tmp <- tempfile(pattern=paste0(name, "_", version), fileext=".tar.gz")
44 cmd <- paste0("wget -q -O '", tmp, "' '", url, "'")
45 cmd <- paste0(cmd, " && nix-hash --type sha256 --base32 --flat '", tmp, "'")
46 cmd <- paste0(cmd, " && echo >&2 ' added ", name, " v", version, "'")
47 cmd <- paste0(cmd, " ; rm -rf '", tmp, "'")
48 system(cmd, intern=TRUE)
49 }
50
51}
52
53escapeName <- function(name) {
54 switch(name, "import" = "r_import", "assert" = "r_assert", name)
55}
56
57formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
58 attr <- gsub(".", "_", escapeName(name), fixed=TRUE)
59 options(warn=5)
60 depends <- paste( if (is.na(depends)) "" else gsub("[ \t\n]+", "", depends)
61 , if (is.na(imports)) "" else gsub("[ \t\n]+", "", imports)
62 , if (is.na(linkingTo)) "" else gsub("[ \t\n]+", "", linkingTo)
63 , sep=","
64 )
65 depends <- unlist(strsplit(depends, split=",", fixed=TRUE))
66 depends <- lapply(depends, gsub, pattern="([^ \t\n(]+).*", replacement="\\1")
67 depends <- lapply(depends, gsub, pattern=".", replacement="_", fixed=TRUE)
68 depends <- depends[depends %in% knownPackages]
69 depends <- lapply(depends, escapeName)
70 depends <- paste(depends)
71 depends <- paste(sort(unique(depends)), collapse=" ")
72 paste0(" ", attr, " = derive2 { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
73}
74
75clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "knownPackages"))
76
77pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates"), method="libcurl"))
78pkgs <- pkgs[order(Package)]
79
80write(paste("updating", mirrorType, "packages"), stderr())
81pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))
82nix <- apply(pkgs, 1, function(p) formatPackage(p[1], p[2], p[18], p[4], p[5], p[6]))
83write("done", stderr())
84
85# Mark deleted packages as broken
86setkey(readFormatted, V2)
87markBroken <- function(name) {
88 str <- paste0(readFormatted[name], collapse='"')
89 if(sum(grep("broken = true;", str)))
90 return(str)
91 write(paste("marked", name, "as broken"), stderr())
92 gsub("};$", "broken = true; };", str)
93}
94broken <- lapply(setdiff(readFormatted[[2]], pkgs[[1]]), markBroken)
95
96cat("# This file is generated from generate-r-packages.R. DO NOT EDIT.\n")
97cat("# Execute the following command to update the file.\n")
98cat("#\n")
99cat(paste("# Rscript generate-r-packages.R", mirrorType, ">new && mv new", packagesFile))
100cat("\n\n")
101cat("{ self, derive }:\n")
102cat("let derive2 = derive ")
103if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
104} else if (mirrorType == "irkernel") { cat("{}")
105} else { cat("{ biocVersion = \"", biocVersion, "\"; }", sep="") }
106cat(";\n")
107cat("in with self; {\n")
108cat(paste(nix, collapse="\n"), "\n", sep="")
109cat(paste(broken, collapse="\n"), "\n", sep="")
110cat("}\n")
111
112stopCluster(cl)