From 3e6b47a0073ec41e6b89f25f5c407a51d7920f9f Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 3 Apr 2023 15:24:07 +1000
Subject: [PATCH] rPackages: switch to official CRAN mirrors

---
 pkgs/build-support/fetchurl/mirrors.nix          |  5 +++++
 pkgs/development/r-modules/default.nix           |  7 ++++---
 pkgs/development/r-modules/generate-r-packages.R | 14 +++++++-------
 pkgs/development/r-modules/generate-shell.nix    |  1 -
 4 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/pkgs/build-support/fetchurl/mirrors.nix b/pkgs/build-support/fetchurl/mirrors.nix
index 3a765089bd2e..bd338473508a 100644
--- a/pkgs/build-support/fetchurl/mirrors.nix
+++ b/pkgs/build-support/fetchurl/mirrors.nix
@@ -43,6 +43,11 @@
     "http://bioconductor.jp/packages/"
   ];
 
+  # CRAN mirrors
+  cran = [
+    "https://cran.r-project.org/src/contrib/"
+  ];
+
   # BitlBee mirrors, see https://www.bitlbee.org/main.php/mirrors.html
   bitlbee = [
     "https://get.bitlbee.org/"
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index d85efc230546..aa7014cf4452 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -68,9 +68,10 @@ let
     hydraPlatforms = [];
   };
   deriveCran = mkDerive {
-    mkHomepage = {name, snapshot, ...}: "https://cran.r-project.org/${snapshot}/web/packages/${name}/";
-    mkUrls = {name, version, snapshot}: [
-      "https://packagemanager.rstudio.com/cran/${snapshot}/src/contrib/${name}_${version}.tar.gz"
+    mkHomepage = {name, ...}: "https://cran.r-project.org/web/packages/${name}/";
+    mkUrls = {name, version}: [
+      "mirror://cran/${name}_${version}.tar.gz"
+      "mirror://cran/Archive/${name}/${name}_${version}.tar.gz"
     ];
   };
 
diff --git a/pkgs/development/r-modules/generate-r-packages.R b/pkgs/development/r-modules/generate-r-packages.R
index 0b01c09a278e..2395329a645a 100755
--- a/pkgs/development/r-modules/generate-r-packages.R
+++ b/pkgs/development/r-modules/generate-r-packages.R
@@ -1,6 +1,5 @@
 #!/usr/bin/env Rscript
 library(data.table)
-library(jsonlite)
 library(parallel)
 library(BiocManager)
 cl <- makeCluster(10)
@@ -12,13 +11,11 @@ if ("release" %in% biocVersion$BiocStatus) {
 } else {
   biocVersion <-  max(as.numeric(as.character(biocVersion$Bioc)))
 }
-dates <- stream_in(url("https://packagemanager.rstudio.com/__api__/repos/2/transaction-dates"), verbose = FALSE)
-snapshotDate <- as.Date(dates[nrow(dates), "alias"])
 
 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("https://packagemanager.rstudio.com/cran/", snapshotDate, "/src/contrib/")
+                  , cran="https://cran.r-project.org/src/contrib/"
                   )
 
 mirrorType <- commandArgs(trailingOnly=TRUE)[1]
@@ -44,6 +41,10 @@ nixPrefetch <- function(name, version) {
     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, "'")
@@ -74,9 +75,8 @@ formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
     paste0("  ", attr, " = derive2 { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
 }
 
-clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "knownPackages"))
+clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "mirrorType", "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())
@@ -102,7 +102,7 @@ cat(paste("# Rscript generate-r-packages.R", mirrorType, ">new && mv new", packa
 cat("\n\n")
 cat("{ self, derive }:\n")
 cat("let derive2 = derive ")
-if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
+if (mirrorType == "cran") { cat("{  }")
 } else if (mirrorType == "irkernel") { cat("{}")
 } else { cat("{ biocVersion = \"", biocVersion, "\"; }", sep="") }
 cat(";\n")
diff --git a/pkgs/development/r-modules/generate-shell.nix b/pkgs/development/r-modules/generate-shell.nix
index 0ab3d6fb557f..1c96cf05cb54 100644
--- a/pkgs/development/r-modules/generate-shell.nix
+++ b/pkgs/development/r-modules/generate-shell.nix
@@ -15,7 +15,6 @@ stdenv.mkDerivation {
     (rWrapper.override {
       packages = with rPackages; [
         data_table
-        jsonlite
         parallel
         BiocManager
       ];