- 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
This commit is contained in:
Pjotr Prins 2008-08-29 13:53:28 +00:00
parent a0e87d6123
commit 73d2e4f49d
12 changed files with 203 additions and 14 deletions

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@ -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";
};
}

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@ -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/;
};
}

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@ -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";

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@ -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";
};
};
}

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@ -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";

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@ -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";
}

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@ -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];
}

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@ -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

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@ -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

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@ -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";
};
}

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@ -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 [];
}

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@ -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