- 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

12 files changed, 203 insertions, 14 deletions

diff --git a/pkgs/applications/networking/cluster/rq/default.nix b/pkgs/applications/networking/cluster/rq/default.nix
new file mode 100644
index 000000000000..7451042b6da7
--- /dev/null
+++ b/pkgs/applications/networking/cluster/rq/default.nix
@@ -0,0 +1,19 @@
+{stdenv, fetchurl, sqlite, ruby }:
+
+stdenv.mkDerivation {
+  name = "rq-3.4.0";
+  src = fetchurl {
+    url = http://www.codeforpeople.com/lib/ruby/rq/rq-3.4.0.tgz;
+    sha256 = "1g8wiv83dcn4vzk9wjjzs9vjnwzwpy4h84h34cj32wfz793wfb8b";
+  };
+
+  buildInputs = [ ruby ];
+
+  installPhase = "ruby install.rb";
+  
+  meta = {
+    license = "Ruby";
+    homepage = "http://www.codeforpeople.com/lib/ruby/rq/";
+    description = "rq is a tool used to create instant linux clusters by managing sqlite databases as nfs mounted priority work queues";
+  };
+}
diff --git a/pkgs/development/interpreters/r-lang/default.nix b/pkgs/development/interpreters/r-lang/default.nix
index 8cf7cce28806..63971dece1f2 100644
--- a/pkgs/development/interpreters/r-lang/default.nix
+++ b/pkgs/development/interpreters/r-lang/default.nix
@@ -1,19 +1,28 @@
-{stdenv, fetchurl, readline, perl, gfortran, libX11, libpng, libXt, zlib}:
+{stdenv, fetchurl, readline, perl, gfortran, libX11, libpng, libXt, zlib, 
+withBioconductor ? false
+}:
 
 stdenv.mkDerivation {
-  name = "r-lang-2.7.0";
+  name = "r-lang";
+  version = "2.7.0";
   src = fetchurl {
     url = http://cran.r-project.org/src/base/R-2/R-2.7.0.tar.gz;
     sha256 = "17ql1j5d9rfpxs04j9v9qyxiysc9nh6yr43lgfdamayzjpia5jqm";
   };
 
+  bioconductor = if withBioconductor then import ../development/libraries/science/biology/bioconductor { inherit fetchurl stdenv readline; } else null;
+  
   buildInputs = [readline perl gfortran libpng libX11 libXt zlib];
   configureFlags = ["--enable-R-shlib"] ;
 
-	meta = {
-		description = "R is a language and environment for statistical computing and graphics";
-		longDescription = ''R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language. R 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.'';
-	  license     = "GPL2";
+  meta = {
+    description = "R is a language and environment for statistical computing and graphics";
+    longDescription = ''R is a language and environment for statistical computin
+g and graphics. It is a GNU project which is similar to the S language. R provid
+es a wide variety of statistical (linear and nonlinear modelling, classical stat
+istical tests, time-series analysis, classification, clustering, ...) and graphi
+cal techniques, and is highly extensible.'';
+    license     = "GPL2";
     homepage    = http://www.r-project.org/;
   };
 }
diff --git a/pkgs/development/libraries/gmp/default.nix b/pkgs/development/libraries/gmp/default.nix
index 48d3446b7810..78839f35ad22 100644
--- a/pkgs/development/libraries/gmp/default.nix
+++ b/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";
diff --git a/pkgs/development/libraries/science/biology/bioconductor/bioconductor.nix b/pkgs/development/libraries/science/biology/bioconductor/bioconductor.nix
new file mode 100644
index 000000000000..d48511cead39
--- /dev/null
+++ b/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";
+     };
+  };
+
+    
+}
diff --git a/pkgs/development/libraries/sqlite/default.nix b/pkgs/development/libraries/sqlite/default.nix
index 087372a6617b..b6cede8e1489 100644
--- a/pkgs/development/libraries/sqlite/default.nix
+++ b/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";
diff --git a/pkgs/development/python-modules/4suite/default.nix b/pkgs/development/python-modules/4suite/default.nix
new file mode 100644
index 000000000000..9f900e4f50ab
--- /dev/null
+++ b/pkgs/development/python-modules/4suite/default.nix
@@ -0,0 +1,13 @@
+{stdenv, fetchurl, python}:
+
+stdenv.mkDerivation rec {
+  version = "1.0.2";
+  name = "4suite-${version}";
+  src = fetchurl {
+    url = "mirror://sourceforge/foursuite/4Suite-XML-${version}.tar.bz2";
+    sha256 = "0g5cyqxhhiqnvqk457k8sb97r18pwgx6gff18q5296xd3zf4cias";
+  };
+  buildInputs = [python];
+  buildPhase = "true";
+  installPhase = "python ./setup.py install --prefix=$out";
+}
diff --git a/pkgs/development/python-modules/zope/default.nix b/pkgs/development/python-modules/zope/default.nix
new file mode 100644
index 000000000000..3dc5da98e769
--- /dev/null
+++ b/pkgs/development/python-modules/zope/default.nix
@@ -0,0 +1,15 @@
+{stdenv, fetchurl, python}:
+
+stdenv.mkDerivation rec {
+	version = "3.2.1";
+  name = "zope-${version}";
+  src = fetchurl {
+	  url = "http://www.zope.org/Products/Zope3/${version}/Zope-${version}.tgz";
+    sha256 = "8431984af75054e4ddfe45bf708924240f8b6b02220cd84d090138413ac82341";
+  };
+  patches = [
+    ./zope_python-2.4.4.patch
+    ./zope_python-readline.patch
+  ];
+  buildInputs = [python];
+}
diff --git a/pkgs/development/python-modules/zope/zope_python-2.4.4.patch b/pkgs/development/python-modules/zope/zope_python-2.4.4.patch
new file mode 100644
index 000000000000..223604129641
--- /dev/null
+++ b/pkgs/development/python-modules/zope/zope_python-2.4.4.patch
@@ -0,0 +1,12 @@
+diff -r 8833d4892dfc Zope-3.2.1/configure
+--- a/configure	Mon Aug 18 14:55:39 2008 +0200
++++ b/configure	Mon Aug 18 14:57:39 2008 +0200
+@@ -21,7 +21,7 @@ prefix="$DEFAULT_PREFIX"
+ 
+ # Place the optimal target version number (as returned by sys.version)
+ # below
+-TARGET="2.4.2"
++TARGET="2.4.4"
+ 
+ # Order a list of "acceptable" python version numbers (as returned by
+ # sys.version) below in "best" to "worst" order, not including the
diff --git a/pkgs/development/python-modules/zope/zope_python-readline.patch b/pkgs/development/python-modules/zope/zope_python-readline.patch
new file mode 100644
index 000000000000..4775cfba49b9
--- /dev/null
+++ b/pkgs/development/python-modules/zope/zope_python-readline.patch
@@ -0,0 +1,12 @@
+diff -r 8833d4892dfc Zope-3.2.1/Dependencies/zope.publisher-Zope-3.2.1/zope.publisher/http.py
+--- a/Dependencies/zope.publisher-Zope-3.2.1/zope.publisher/http.py	Mon Aug 18 14:55:39 2008 +0200
++++ b/Dependencies/zope.publisher-Zope-3.2.1/zope.publisher/http.py	Mon Aug 18 16:37:02 2008 +0200
+@@ -198,7 +198,7 @@ class HTTPInputStream(object):
+         self.cacheStream.write(data)
+         return data
+ 
+-    def readline(self):
++    def readline(self, size=None):
+         data = self.stream.readline()
+         self.cacheStream.write(data)
+         return data
diff --git a/pkgs/development/tools/misc/unifdef/default.nix b/pkgs/development/tools/misc/unifdef/default.nix
new file mode 100644
index 000000000000..7ba421b14a47
--- /dev/null
+++ b/pkgs/development/tools/misc/unifdef/default.nix
@@ -0,0 +1,24 @@
+{ fetchurl, stdenv }:
+
+stdenv.mkDerivation {
+  name = "unifdef-1.0";
+
+  src = fetchurl {
+    url = http://freshmeat.net/redir/unifdef/10933/url_tgz/unifdef-1.0.tar.gz;
+    sha256 = "d14c30b1e2e9745e4b067ab86337c93ad907b4e9ee1c414d45291bf7f0c19dad";
+  };
+
+  buildPhase = ''
+    make unifdef
+  '';
+
+  installPhase = ''
+    ensureDir $out/bin
+    cp unifdef $out/bin
+  '';
+
+  meta = {
+    description = "useful for removing #ifdef'ed lines from a file while otherwise leaving the file alone";
+
+  };
+}
diff --git a/pkgs/os-specific/linux/kernel-headers/2.6.18.5.nix b/pkgs/os-specific/linux/kernel-headers/2.6.18.5.nix
new file mode 100644
index 000000000000..cf4efd159e8f
--- /dev/null
+++ b/pkgs/os-specific/linux/kernel-headers/2.6.18.5.nix
@@ -0,0 +1,23 @@
+{stdenv, fetchurl, unifdef}:
+
+assert stdenv.isLinux;
+
+stdenv.mkDerivation {
+  name = "linux-headers-2.6.18.5";
+  builder = ./builder.sh;
+  src = fetchurl {
+    url = "mirror://kernel/linux/kernel/v2.6/linux-2.6.18.5.tar.bz2";
+    sha256 = "24f0e0011cdae42e3dba56107bb6a60c57c46d1d688a9b0300fec53e80fd1e53";
+  };
+
+  buildInputs = [ unifdef ];
+
+  platform = 
+    if stdenv.system == "i686-linux" then "i386" else
+    if stdenv.system == "x86_64-linux" then "x86_64" else
+    if stdenv.system == "powerpc-linux" then "powerpc" else
+    abort "don't know what the kernel include directory is called for this platform";
+
+  extraIncludeDirs =
+    if stdenv.system == "powerpc-linux" then ["ppc"] else [];
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index e687d8ed3f25..6fa4bbc144f7 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -570,6 +570,10 @@ let
     stdenv = stdenvNew;
   };
 
+  unifdef = import ../development/tools/misc/unifdef {
+    inherit fetchurl stdenv;
+  };
+
   coreutils = useFromStdenv "coreutils"
     ((if stdenv ? isDietLibC
       then import ../tools/misc/coreutils-5
@@ -2032,12 +2036,17 @@ let
   rLang = import ../development/interpreters/r-lang {
     inherit fetchurl stdenv readline perl gfortran libpng zlib;
     inherit (xorg) libX11 libXt;
+    withBioconductor = getConfig ["rLang" "withBioconductor"] false;
   };
 
   rubygems = builderDefsPackage (import ../development/interpreters/ruby/gems.nix) {
     inherit ruby makeWrapper;
   };
 
+  rq = import ../applications/networking/cluster/rq {
+    inherit fetchurl stdenv sqlite ruby;
+  };
+
   spidermonkey = import ../development/interpreters/spidermonkey {
     inherit fetchurl stdenv readline;
   };
@@ -3543,7 +3552,7 @@ let
   };
 
   sqlite = import ../development/libraries/sqlite {
-    inherit fetchurl stdenv;
+    inherit fetchurl stdenv readline;
   };
 
   t1lib = import ../development/libraries/t1lib {
@@ -4505,6 +4514,10 @@ let
   ### DEVELOPMENT / PYTHON MODULES
 
 
+  foursuite = import ../development/python-modules/4suite {
+    inherit fetchurl stdenv python;
+  };
+
   bsddb3 = import ../development/python-modules/bsddb3 {
     inherit fetchurl stdenv python db4;
   };
@@ -4596,6 +4609,9 @@ let
     inherit fetchurl stdenv python;
   };
 
+  zope = import ../development/python-modules/zope {
+    inherit fetchurl stdenv python;
+  };
 
   ### SERVERS