r-modules: use HTTPS, allow passing args from generated set, use MRAN

pkgs/development/r-modules/default.nix

@@ -11,7 +11,10 @@ let
   #
   # some packages, e.g. cncaGUI, require X running while installation,
   # so that we use xvfb-run if requireX is true.
-  mkDerive = {mkHomepage, mkUrls}: lib.makeOverridable ({
+  mkDerive = {mkHomepage, mkUrls}: args:
+      # XXX: not ideal ("2.2" would match "2.22") but sufficient
+      assert (!(args ? rVersion) || lib.hasPrefix args.rVersion (lib.getVersion R));
+      lib.makeOverridable ({
         name, version, sha256,
         depends ? [],
         doCheck ? true,
@@ -22,12 +25,12 @@ let
     name = "${name}-${version}";
     src = fetchurl {
       inherit sha256;
-      urls = mkUrls { inherit name version; };
+      urls = mkUrls (args // { inherit name version; });
     };
     inherit doCheck requireX;
     propagatedBuildInputs = depends;
     nativeBuildInputs = depends;
-    meta.homepage = mkHomepage name;
+    meta.homepage = mkHomepage (args // { inherit name; });
     meta.platforms = R.meta.platforms;
     meta.hydraPlatforms = hydraPlatforms;
     meta.broken = broken;
@@ -37,18 +40,15 @@ let
   # from the name, version, sha256, and optional per-package arguments above
   #
   deriveBioc = mkDerive {
-    mkHomepage = name: "http://cran.r-project.org/web/packages/${name}/";
-    mkUrls = {name, version}: [ "mirror://bioc/src/contrib/${name}_${version}.tar.gz" ];
+    mkHomepage = {name, rVersion}: "https://bioconductor.org/packages/${rVersion}/bioc/html/${name}.html";
+    mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/bioc/src/contrib/${name}_${version}.tar.gz" ];
   };
   deriveCran = mkDerive {
-    mkHomepage = name: "http://bioconductor.org/packages/release/bioc/html/${name}.html";
-    mkUrls = {name, version}: [
-      "mirror://cran/src/contrib/${name}_${version}.tar.gz"
-      "mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz"
-    ];
+    mkHomepage = {name, snapshot}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/";
+    mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ];
   };
   deriveIRkernel = mkDerive {
-    mkHomepage = name: "http://irkernel.github.io/";
+    mkHomepage = {name}: "https://irkernel.github.io/";
     mkUrls = {name, version}: [ "http://irkernel.github.io/src/contrib/${name}_${version}.tar.gz" ];
   };
 

pkgs/development/r-modules/generate-r-packages.R

@@ -7,14 +7,16 @@ mirrorType <- commandArgs(trailingOnly=TRUE)[1]
 stopifnot(mirrorType %in% c("bioc","cran", "irkernel"))
 
 packagesFile <- paste(mirrorType, 'packages.nix', sep='-')
-readFormatted <- as.data.table(read.table(skip=6, sep='"', text=head(readLines(packagesFile), -1)))
+readFormatted <- as.data.table(read.table(skip=8, sep='"', text=head(readLines(packagesFile), -1)))
+rVersion <- paste(R.Version()$major, strsplit(R.Version()$minor, ".", fixed=TRUE)[[1]][1], sep=".")
+snapshotDate <- Sys.Date()
 
-mirrorUrls <- list( bioc="http://bioconductor.statistik.tu-dortmund.de/packages/3.2/bioc/src/contrib/"
-                  , cran="http://cran.r-project.org/src/contrib/"
-                  , irkernel="http://irkernel.github.io/src/contrib/"
+mirrorUrls <- list( bioc=paste0("https://bioconductor.statistik.tu-dortmund.de/packages/", rVersion, "/bioc/src/contrib/")
+                  , cran=paste0("https://mran.revolutionanalytics.com/snapshot/", snapshotDate, "/src/contrib/")
+                  , irkernel="https://irkernel.github.io/src/contrib/"
                   )
 mirrorUrl <- mirrorUrls[mirrorType][[1]]
-knownPackages <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates"))))
+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))
@@ -38,12 +40,12 @@ formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
     depends <- sapply(depends, gsub, pattern=".", replacement="_", fixed=TRUE)
     depends <- depends[depends %in% knownPackages]
     depends <- paste(sort(unique(depends)), collapse=" ")
-    paste0(attr, " = derive { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
+    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")))
+pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates"), method="libcurl"))
 pkgs <- pkgs[order(Package)]
 pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))
 
@@ -54,8 +56,14 @@ 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 }: with self; {\n")
-cat(paste(nix, collapse="\n"), "\n")
+cat("{ self, derive }:\n")
+cat("let derive2 = derive ")
+if (mirrorType == "bioc") { cat("{ rVersion = \"", rVersion, "\"; }", sep="")
+} else if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
+} else if (mirrorType == "irkernel") { cat("{}") }
+cat(";\n")
+cat("in with self; {\n")
+cat(paste(nix, collapse="\n"), "\n", sep="")
 cat("}\n")
 
 stopCluster(cl)

pkgs/development/r-modules/generate-shell.nix

@@ -0,0 +1,16 @@
+with import <nixpkgs> {};
+
+stdenv.mkDerivation {
+  name = "generate-r-packages-shell";
+
+  buildCommand = "exit 1";
+
+  nativeBuildInputs = [ 
+    (rWrapper.override {
+      packages = with rPackages; [
+        data_table
+        parallel
+      ];
+    })
+  ];
+}