- Some Ruby interpreter bumped version

- Kernel headers 2.6.18 added (XEN virtual images)
- unifdef package added for kernel headers 2.6.18
- Python Zope and 4suite added
- Trying bioconductor packages with R-lang (still failing)
- Bumped gmp version
- Added rq cluster runner - still requires extra gems (installs, but does not run)


svn path=/nixpkgs/trunk/; revision=12766

pkgs/development/libraries/gmp/default.nix

@@ -1,16 +1,17 @@
-{stdenv, fetchurl, m4, cxx ? true}:
+{stdenv, fetchurl, m4, cxx ? true }:
 
 stdenv.mkDerivation {
-  name = "gmp-4.2.2";
+  name = "gmp-4.2.3";
 
   src = fetchurl {
-    url = mirror://gnu/gmp/gmp-4.2.2.tar.bz2;
-    sha256 = "0yv593sk62ypn21gg2x570g955lmsi4i6f2bc3s43p52myn0lb1b";
+    url = mirror://gnu/gmp/gmp-4.2.3.tar.bz2;
+    sha256 = "139b5abc49833832184c0a03ff6fc64c59ef102b420d2a5884ad78af5647414b";
   };
 
-  buildInputs = [m4];
+  buildInputs = [m4 stdenv.gcc.libc ];
   configureFlags = if cxx then "--enable-cxx" else "--disable-cxx";
   doCheck = true;
+  postBuild = "make check";  # Test the compiler for being correct
 
   meta = {
     description = "A free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers";

pkgs/development/libraries/science/biology/bioconductor/bioconductor.nix

@@ -0,0 +1,43 @@
+{stdenv, fetchurl, rLang}:
+
+let
+
+  /* Function to compile Bioconductor packages */
+
+  buildBioConductor =
+    { pname, pver, src, postInstall ? ""}:
+
+    stdenv.mkDerivation {
+      name = "${pname}-${pver}";
+
+      inherit src;
+
+      buildInputs = [rLang];
+
+      # dontAddPrefix = true;
+
+      # preBuild = "makeFlagsArray=(dictdir=$out/lib/aspell datadir=$out/lib/aspell)";
+
+      inherit postInstall;
+      installPhase = ''
+        R CMD INSTALL ${affyioSrc}
+      '';
+
+      meta = {
+        description = "Bioconductor package for ${pname}";
+      };
+    };
+
+in {
+
+   affyio = buildBioC {
+     pname = "affyio";
+     pver  = "1.8.1";
+     src = fetchurl {
+       url = http://www.bioconductor.org/packages/release/bioc/src/contrib/affyio_1.8.1.tar.gz;
+       sha256 = "136nkpq870vrwf9z5gq32xjzrp8bjfbk9pn8fki2a5w2lr0qc8nh";
+     };
+  };
+
+    
+}

pkgs/development/libraries/sqlite/default.nix

@@ -1,4 +1,4 @@
-{stdenv, fetchurl}:
+{stdenv, fetchurl, readline}:
 
 stdenv.mkDerivation {
   name = "sqlite-3.5.9";
@@ -9,7 +9,9 @@ stdenv.mkDerivation {
     url = http://www.sqlite.org/sqlite-3.5.9.tar.gz;
     sha256 = "0731zj0fnivhfc74wc3yh0p9gn7fpjgy3g79haarciqkdf8k3lvx";
   };
-  
+
+  buildInputs = [readline];
+
   meta = {
     homepage = http://www.sqlite.org/;
     description = "A self-contained, serverless, zero-configuration, transactional SQL database engine";