R: add various features

* Ensure that R can link blas, liblapack, and libgfortran at run-time.
* Ensure that R can run the Tcl/Tk interpreter.
* Add Java support.
* Install texinfo and PDF documentation.

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

···
 { stdenv, fetchurl, blas, bzip2, gfortran, liblapack, libX11, libXmu, libXt
 , libjpeg, libpng, libtiff, ncurses, pango, pcre, perl, readline, tcl
-, texLive, tk, xz, zlib, less, texinfo, graphviz
+, texLive, tk, xz, zlib, less, texinfo, graphviz, icu, pkgconfig, bison
+, imake, which, jdk, atlas
 }:
 
 stdenv.mkDerivation rec {
···
 
   buildInputs = [ blas bzip2 gfortran liblapack libX11 libXmu libXt
     libXt libjpeg libpng libtiff ncurses pango pcre perl readline tcl
-    texLive tk xz zlib less texinfo graphviz ];
+    texLive tk xz zlib less texinfo graphviz icu pkgconfig bison imake
+    which jdk atlas
+  ];
+
+  patches = [ ./no-usr-local-search-paths.patch ];
+
+  preConfigure = ''
+    configureFlagsArray=(
+      --disable-lto
+      --with-blas="-L${atlas}/lib -lf77blas -latlas"
+      --with-lapack="-L${liblapack}/lib -llapack"
+      --with-readline
+      --with-tcltk --with-tcl-config="${tcl}/lib/tclConfig.sh" --with-tk-config="${tk}/lib/tkConfig.sh"
+      --with-cairo
+      --with-libpng
+      --with-jpeglib
+      --with-libtiff
+      --with-system-zlib
+      --with-system-bzlib
+      --with-system-pcre
+      --with-system-xz
+      --with-ICU
+      R_SHELL="${stdenv.shell}"
+      JAVA_HOME="${jdk}"
+      LDFLAGS="-L${gfortran.gcc}/lib"
+    )
+    echo "TCLLIBPATH=${tk}/lib" >>etc/Renviron.in
+  '';
+
+  installTargets = [ "install" "install-info" "install-pdf" ];
+
+  doCheck = true;
 
   enableParallelBuilding = true;
 
   meta = {
-    description = "a free software environment for statistical computing and graphics";
     homepage = "http://www.r-project.org/";
+    description = "a free software environment for statistical computing and graphics";
     license = stdenv.lib.licenses.gpl2Plus;
+
+    longDescription = ''
+      GNU R is a language and environment for statistical computing and
+      graphics that provides a wide variety of statistical (linear and
+      nonlinear modelling, classical statistical tests, time-series
+      analysis, classification, clustering, ...) and graphical
+      techniques, and is highly extensible. One of R's strengths is the
+      ease with which well-designed publication-quality plots can be
+      produced, including mathematical symbols and formulae where
+      needed. R is an integrated suite of software facilities for data
+      manipulation, calculation and graphical display. It includes an
+      effective data handling and storage facility, a suite of operators
+      for calculations on arrays, in particular matrices, a large,
+      coherent, integrated collection of intermediate tools for data
+      analysis, graphical facilities for data analysis and display
+      either on-screen or on hardcopy, and a well-developed, simple and
+      effective programming language which includes conditionals, loops,
+      user-defined recursive functions and input and output facilities.
+    '';
 
     platforms = stdenv.lib.platforms.linux;
     maintainers = [ stdenv.lib.maintainers.simons ];

pkgs/applications/science/math/R/no-usr-local-search-paths.patch

···
+diff -ubr R-3.0.1-orig/configure R-3.0.1/configure
+--- R-3.0.1-orig/configure	2013-07-04 10:46:42.336133947 +0200
++++ R-3.0.1/configure	2013-07-04 10:46:17.181919960 +0200
+@@ -3800,13 +3800,13 @@
+ : ${LIBnn=$libnn}
+ ## We provide these defaults so that headers and libraries in
+ ## '/usr/local' are found (by the native tools, mostly).
+-if test -f "/sw/etc/fink.conf"; then
+-  : ${CPPFLAGS="-I/sw/include -I/usr/local/include"}
+-  : ${LDFLAGS="-L/sw/lib -L/usr/local/lib"}
+-else
+-  : ${CPPFLAGS="-I/usr/local/include"}
+-  : ${LDFLAGS="-L/usr/local/${LIBnn}"}
+-fi
++# if test -f "/sw/etc/fink.conf"; then
++#   : ${CPPFLAGS="-I/sw/include -I/usr/local/include"}
++#   : ${LDFLAGS="-L/sw/lib -L/usr/local/lib"}
++# else
++#   : ${CPPFLAGS="-I/usr/local/include"}
++#   : ${LDFLAGS="-L/usr/local/${LIBnn}"}
++# fi
+ 
+ ## take care not to  override the command-line setting
+ if test "${libdir}" = '${exec_prefix}/lib'; then