Merge pull request #22817 from jbedo/r

R: 3.2.4 -> 3.3.2

pkgs/applications/science/math/R/default.nix

@@ -7,11 +7,11 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "R-3.2.4";
+  name = "R-3.3.2";
 
   src = fetchurl {
     url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
-    sha256 = "0l6k3l3cy6fa9xkn23zvz5ykpw10s45779x88yz3pzn2x5gl1zds";
+    sha256 = "0k2i9qdd83g09fcpls2198q4ykxkii5skczb514gnx7mx4hsv56j";
   };
 
   buildInputs = [ bzip2 gfortran libX11 libXmu libXt
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
     ++ stdenv.lib.optionals (!stdenv.isDarwin) [ tcl tk ]
     ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation cf-private libobjc ];
 
-  patches = [ ./no-usr-local-search-paths.patch ];
+  patches = [ ./no-usr-local-search-paths.patch ./zlib-version-check.patch ];
 
   preConfigure = ''
     configureFlagsArray=(
@@ -35,10 +35,6 @@ stdenv.mkDerivation rec {
       --with-libpng
       --with-jpeglib
       --with-libtiff
-      --with-system-zlib
-      --with-system-bzlib
-      --with-system-pcre
-      --with-system-xz
       --with-ICU
       ${stdenv.lib.optionalString enableStrictBarrier "--enable-strict-barrier"}
       --enable-R-shlib
@@ -69,7 +65,7 @@ stdenv.mkDerivation rec {
 
   installTargets = [ "install" "install-info" "install-pdf" ];
 
-  doCheck = true;
+  doCheck = withRecommendedPackages;
 
   enableParallelBuilding = true;
 

pkgs/applications/science/math/R/zlib-version-check.patch

@@ -0,0 +1,20 @@
+diff --git a/configure b/configure
+index cf368ce..dc528ff 100755
+--- a/configure
++++ b/configure
+@@ -35507,10 +35507,11 @@ else
+ #include <string.h>
+ #include <zlib.h>
+ int main() {
+-#ifdef ZLIB_VERSION
+-/* Work around Debian bug: it uses 1.2.3.4 even though there was no such
+-   version on the master site zlib.net */
+-  exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
++#ifdef ZLIB_VERNUM
++  if (ZLIB_VERNUM < 0x01250) {
++    exit(1);
++  }
++  exit(0);
+ #else
+   exit(1);
+ #endif

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

@@ -4,7 +4,7 @@ library(parallel)
 cl <- makeCluster(10)
 
 rVersion <- paste(R.Version()$major, strsplit(R.Version()$minor, ".", fixed=TRUE)[[1]][1], sep=".")
-snapshotDate <- Sys.Date()
+snapshotDate <- Sys.Date()-1
 
 mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", rVersion, "/bioc/src/contrib/")
                   , "bioc-annotation"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", rVersion, "/data/annotation/src/contrib/")
@@ -45,16 +45,20 @@ nixPrefetch <- function(name, version) {
 }
 
 formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
+    name <- ifelse(name == "import", "r_import", name)
     attr <- gsub(".", "_", 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 <- sapply(depends, gsub, pattern="([^ \t\n(]+).*", replacement="\\1")
-    depends <- sapply(depends, gsub, pattern=".", replacement="_", 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, function(d) ifelse(d == "import", "r_import", d))
+    depends <- paste(depends)
     depends <- paste(sort(unique(depends)), collapse=" ")
     paste0("  ", attr, " = derive2 { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
 }