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

4 files changed, 53 insertions, 134 deletions

diff --git a/pkgs/build-support/fetchurl/mirrors.nix b/pkgs/build-support/fetchurl/mirrors.nix
index 14b4d6fc9a27..9a3cdd5c77d2 100644
--- a/pkgs/build-support/fetchurl/mirrors.nix
+++ b/pkgs/build-support/fetchurl/mirrors.nix
@@ -300,120 +300,15 @@ rec {
   # The commented-out ones don't seem to allow direct package downloads;
   # they serve error messages that result in hash mismatches instead.
   bioc = [
-    # http://bioc.ism.ac.jp/3.2/bioc/
-    # http://bioc.openanalytics.eu/3.2/bioc/
-    # http://bioconductor.fmrp.usp.br/3.2/bioc/
-    # http://mirror.aarnet.edu.au/pub/bioconductor/3.2/bioc/
-    # http://watson.nci.nih.gov/bioc_mirror/3.2/bioc/
-    http://bioconductor.jp/packages/3.2/bioc/
-    http://bioconductor.statistik.tu-dortmund.de/packages/3.2/bioc/
-    http://mirrors.ebi.ac.uk/bioconductor/packages/3.2/bioc/
-    http://mirrors.ustc.edu.cn/bioc/3.2/bioc/
-  ];
-
-  # CRAN mirrors (from http://cran.r-project.org/mirrors.html)
-  cran = [
-    http://cran.r-project.org/
-    http://cran.rstudio.com/
-    http://cran.usthb.dz/
-    http://mirror.fcaglp.unlp.edu.ar/CRAN/
-    http://cran.csiro.au/
-    http://cran.ms.unimelb.edu.au/
-    http://cran.at.r-project.org/
-    http://www.freestatistics.org/cran/
-    http://nbcgib.uesc.br/mirrors/cran/
-    http://cran-r.c3sl.ufpr.br/
-    http://cran.fiocruz.br/
-    http://www.vps.fmvz.usp.br/CRAN/
-    http://brieger.esalq.usp.br/CRAN/
-    http://cran.stat.sfu.ca/
-    http://mirror.its.dal.ca/cran/
-    http://cran.utstat.utoronto.ca/
-    http://cran.skazkaforyou.com/
-    http://cran.parentingamerica.com/
-    http://dirichlet.mat.puc.cl/
-    http://ftp.ctex.org/mirrors/CRAN/
-    http://mirror.bjtu.edu.cn/cran
-    http://mirrors.ustc.edu.cn/CRAN/
-    http://mirrors.xmu.edu.cn/CRAN/
-    http://www.laqee.unal.edu.co/CRAN/
-    http://www.icesi.edu.co/CRAN/
-    http://mirrors.nic.cz/R/
-    http://mirrors.dotsrc.org/cran/
-    http://cran.espol.edu.ec/
-    http://cran.salud.gob.sv/
-    http://ftp.eenet.ee/pub/cran/
-    http://cran.univ-lyon1.fr/
-    http://mirror.ibcp.fr/pub/CRAN/
-    http://ftp.igh.cnrs.fr/pub/CRAN/
-    http://cran.irsn.fr/
-    http://cran.univ-paris1.fr/
-    http://cran.cardse.net/
-    http://mirrors.softliste.de/cran/
-    http://ftp5.gwdg.de/pub/misc/cran/
-    http://cran.sciserv.eu/
-    http://cran.uni-muenster.de/
-    http://cran.cc.uoc.gr/mirrors/CRAN/
-    http://cran.rapporter.net/
-    http://cran.hafro.is/
-    http://ftp.iitm.ac.in/cran/
-    http://cran.repo.bppt.go.id/
-    http://cran.um.ac.ir/
-    http://ftp.heanet.ie/mirrors/cran.r-project.org/
-    http://cran.mirror.garr.it/mirrors/CRAN/
-    http://cran.stat.unipd.it/
-    http://dssm.unipa.it/CRAN/
-    http://cran.ism.ac.jp/
-    http://cran.md.tsukuba.ac.jp/
-    http://cran.nexr.com/
-    http://healthstat.snu.ac.kr/CRAN/
-    http://cran.biodisk.org/
-    http://rmirror.lau.edu.lb/
-    http://cran.itam.mx/
-    http://www.est.colpos.mx/R-mirror/
-    http://cran.xl-mirror.nl/
-    http://cran-mirror.cs.uu.nl/
-    http://cran.stat.auckland.ac.nz/
-    http://cran.uib.no/
-    http://cran.stat.upd.edu.ph/
-    http://r.meteo.uni.wroc.pl/
-    http://cran.dcc.fc.up.pt/
-    http://cran.gis-lab.info/
-    http://cran.stat.nus.edu.sg/
-    http://cran.fyxm.net/
-    http://r.adu.org.za/
-    http://cran.mirror.ac.za/
-    http://ftp.cixug.es/CRAN/
-    http://cran.es.r-project.org/
-    http://ftp.sunet.se/pub/lang/CRAN/
-    http://stat.ethz.ch/CRAN/
-    http://ftp.yzu.edu.tw/CRAN/
-    http://cran.csie.ntu.edu.tw/
-    http://mirrors.psu.ac.th/pub/cran/
-    http://cran.pau.edu.tr/
-    http://www.stats.bris.ac.uk/R/
-    http://mirrors.ebi.ac.uk/CRAN/
-    http://cran.ma.imperial.ac.uk/
-    http://mirror.mdx.ac.uk/R/
-    http://star-www.st-andrews.ac.uk/cran/
-    http://cran.cnr.berkeley.edu/
-    http://cran.stat.ucla.edu/
-    http://streaming.stat.iastate.edu/CRAN/
-    http://ftp.ussg.iu.edu/CRAN/
-    http://rweb.quant.ku.edu/cran/
-    http://watson.nci.nih.gov/cran_mirror/
-    http://cran.mtu.edu/
-    http://cran.wustl.edu/
-    http://cran.case.edu/
-    http://ftp.osuosl.org/pub/cran/
-    http://lib.stat.cmu.edu/R/CRAN/
-    http://cran.mirrors.hoobly.com/
-    http://mirrors.nics.utk.edu/cran/
-    http://cran.revolutionanalytics.com/
-    http://cran.fhcrc.org/
-    http://cran.cs.wwu.edu/
-    http://camoruco.ing.uc.edu.ve/cran/
-    http://cran.vinastat.com/
+    # http://bioc.ism.ac.jp/
+    # http://bioc.openanalytics.eu/
+    # http://bioconductor.fmrp.usp.br/
+    # http://mirror.aarnet.edu.au/pub/bioconductor/
+    # http://watson.nci.nih.gov/bioc_mirror/
+    http://bioconductor.jp/packages/
+    http://bioconductor.statistik.tu-dortmund.de/packages/
+    http://mirrors.ebi.ac.uk/bioconductor/packages/
+    http://mirrors.ustc.edu.cn/bioc/
   ];
 
   # Hackage mirrors
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 84ae091ee11e..0d30dc4c6b81 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/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" ];
   };
 
diff --git a/pkgs/development/r-modules/generate-r-packages.R b/pkgs/development/r-modules/generate-r-packages.R
index 4c5654184509..d45401b957de 100755
--- a/pkgs/development/r-modules/generate-r-packages.R
+++ b/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)
diff --git a/pkgs/development/r-modules/generate-shell.nix b/pkgs/development/r-modules/generate-shell.nix
new file mode 100644
index 000000000000..43c97e009c7e
--- /dev/null
+++ b/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
+      ];
+    })
+  ];
+}