r-modules: fixing rggobi by adding initial expression for ggobi

pkgs/development/r-modules/default.nix

@@ -267,6 +267,7 @@ let
     rgeos = [ pkgs.geos ];
     rgl = [ pkgs.mesa pkgs.x11 ];
     Rglpk = [ pkgs.glpk ];
+    rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
     RGtk2 = [ pkgs.gtk2 ];
     Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
     ridge = [ pkgs.gsl ];
@@ -339,6 +340,7 @@ let
     WideLM = [ pkgs.cudatoolkit ];
     RCurl = [ pkgs.curl ];
     R2SWF = [ pkgs.pkgconfig ];
+    rggobi = [ pkgs.pkgconfig ];
     RGtk2 = [ pkgs.pkgconfig ];
     RProtoBuf = [ pkgs.pkgconfig ];
     Rpoppler = [ pkgs.pkgconfig ];
@@ -664,7 +666,6 @@ let
     "BcDiag" # requires fabia
     "bdvis" # requres taxize
     "beadarrayFilter" # requires beadarray
-    "beadarrayMSV" # requires rggobi
     "bigGP" # requires MPI running. HELP WANTED!
     "bigpca" # requires NCmisc
     "Biograph" # requires mvna
@@ -680,7 +681,6 @@ let
     "ChemoSpec" # depends on broken speaq
     "classGraph" # requires graph, and Rgraphviz
     "clpAPI" # requires clp
-    "clusterfly" # requires rggobi
     "compendiumdb" # requires Biobase
     "CORM" # requires limma
     "cplexAPI" # requires CPLEX
@@ -821,7 +821,6 @@ let
     "permGPU" # requires Biobase
     "PhViD" # requires LBE
     "pi0" # requires qvalue
-    "PKgraph" # requires rggobi
     "plmDE" # requires limma
     "plsRcox" # requires survcomp
     "PMA" # requires impute
@@ -855,7 +854,6 @@ let
     "REBayes" # requires Rmosek
     "RefFreeEWAS" # requires isva
     "retistruct" # depends on broken RImageJROI
-    "rggobi" # requires GGobi
     "RImageJROI" # requires spatstat
     "rjade" # requires V8 to build
     "rJPSGCS" # requires chopsticks
@@ -886,7 +884,6 @@ let
     "selectspm" # depends on broken ecespa
     "semiArtificial" # requires RSNNS
     "SeqFeatR" # requires Biostrings, qvalue, and widgetTools
-    "SeqGrapheR" # requires rggobi
     "sequenza" # requires copynumber
     "SGCS" # requires spatstat
     "siar" # requires spatstat

pkgs/tools/graphics/ggobi/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, fetchurl, pkgconfig, libxml2, gtk2 }:
+
+stdenv.mkDerivation rec {
+  version = "2.1.11";
+  name = "ggobi-${version}";
+
+  src = fetchurl {
+    url = "http://www.ggobi.org/downloads/ggobi-${version}.tar.bz2";
+    sha256 = "2c4ddc3ab71877ba184523e47b0637526e6f3701bd9afb6472e6dfc25646aed7";
+  };
+
+  buildInputs = [ pkgconfig libxml2 gtk2 ];
+
+  configureFlags = "--with-all-plugins";
+
+  meta = with stdenv.lib; {
+    description = "Visualization program for exploring high-dimensional data";
+    homepage = http://www.ggobi.org/;
+    license = licenses.cpl10;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.michelk ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -1407,6 +1407,8 @@ let
 
   gftp = callPackage ../tools/networking/gftp { };
 
+  ggobi = callPackage ../tools/graphics/ggobi { };
+
   gifsicle = callPackage ../tools/graphics/gifsicle { };
 
   gitlab = callPackage ../applications/version-management/gitlab {