Initial import

(Portage version: 2.1.10.63/cvs/Linux x86_64)

7 files changed, 247 insertions, 0 deletions

diff --git a/sci-libs/shogun/ChangeLog b/sci-libs/shogun/ChangeLog
new file mode 100644
index 000000000000..1e71a1977e81
--- /dev/null
+++ b/sci-libs/shogun/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-libs/shogun
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/ChangeLog,v 1.1 2012/06/14 17:16:03 bicatali Exp $
+
+*shogun-1.1.0 (14 Jun 2012)
+
+  14 Jun 2012; Sébastien Fabbro <bicatali@gentoo.org> +shogun-1.1.0.ebuild,
+  +files/shogun-1.1.0-respect-ldflags.patch,
+  +files/shogun-1.1.0-test-readline.patch,
+  +files/shogun-1.1.0-test-snappy.patch, +metadata.xml:
+  Initial import
+
diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
new file mode 100644
index 000000000000..d031033f89e5
--- /dev/null
+++ b/sci-libs/shogun/Manifest
@@ -0,0 +1,8 @@
+AUX shogun-1.1.0-respect-ldflags.patch 332 RMD160 7da4e7c1d3c1967b80128a85dc4b825657bf0d09 SHA1 2b39db7545c9fc0be983105ad6f197c0724723fe SHA256 596e37d9bac7904808cf5cd58221f97f3ce3e583aed58697b4a4f995c9dd0eff
+AUX shogun-1.1.0-test-readline.patch 352 RMD160 adb00cafbbecdb81240e123a69f15126660975df SHA1 1b1539cd28fd0459b00926a301d18575ca1c9b84 SHA256 a8e0ecc78bf702bdfb8193fc94abd7745e8bfcee0fe1e6b4ba5efeac4c6df0cc
+AUX shogun-1.1.0-test-snappy.patch 506 RMD160 e000b8fdd67c991bde80d8fd29d52e8bcf71e40b SHA1 8af5880abeda1ce4ad73c67d3bc32e8ff6bcf91e SHA256 ef0489b05cd1dd494c4a9b5070277dbd7733b920cfcf045e87d6abcbd871f01f
+DIST shogun-1.1.0.tar.bz2 3485714 RMD160 8744c0463550d3b9b3d023ee5f236f696ca0ede2 SHA1 7847e7b365a06a01d9cd40732ca906ae464f975f SHA256 9f69638f0bc18995358c38cd6eed6437e6b90c1fceab7c6e64c9739b7e6cc40b
+DIST shogun-data-0.3.tar.bz2 126676026 RMD160 2169ddc8f744529a576fcbfc2dd498cf6436cc1a SHA1 feb21b8f3f5cfbeb5c2d7910bc5481e6b0277c44 SHA256 34272e3f5e6b6989a4941b925ab3a9cd1525d73180681884e948a673aff4ef89
+EBUILD shogun-1.1.0.ebuild 4188 RMD160 9a958579ecf1058314080805e4007fd989f7b9b3 SHA1 ac03bc73f89df8dce2075102cde0dd53abaaf79c SHA256 0ea9f48162d0b559f46c3ac01544b2d2d9bdeae9aab36bc9ba05aed9ac8752bf
+MISC ChangeLog 384 RMD160 c38602ed508846b9e9978309c26b4d38d1271917 SHA1 b1d0674f0c4e95f9fdd743e426fc5e2c4c3206d3 SHA256 49786d2d4b8906a0f363a7ab5ee2e29316da26e675493c8776bfc43b3eea6362
+MISC metadata.xml 1928 RMD160 1dbce3b25762793bde5017197bf0df5e090fff05 SHA1 669d72eeccfce0aa397771c3c26a4ea5084c7dff SHA256 3698c29b00d6933893b30da4ff6a0c66444cfbc7bcfcacdb5fae5dea97ac5277
diff --git a/sci-libs/shogun/files/shogun-1.1.0-respect-ldflags.patch b/sci-libs/shogun/files/shogun-1.1.0-respect-ldflags.patch
new file mode 100644
index 000000000000..0e4a331d354c
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-1.1.0-respect-ldflags.patch
@@ -0,0 +1,12 @@
+diff -Nur src.orig/configure src/configure
+--- src.orig/configure	2012-06-12 00:57:14.000000000 +0100
++++ src/configure	2012-06-12 18:13:26.000000000 +0100
+@@ -164,7 +164,7 @@
+ DEFINES="-DSWIG_TYPE_TABLE=shogun -DSHOGUN"
+ DEFINES_SWIG=
+ PRELINKFLAGS=
+-LINKFLAGS=
++LINKFLAGS="$LDFLAGS"
+ POSTLINKFLAGS=
+ 
+ INCLUDES_STATIC_INTERFACES=
diff --git a/sci-libs/shogun/files/shogun-1.1.0-test-readline.patch b/sci-libs/shogun/files/shogun-1.1.0-test-readline.patch
new file mode 100644
index 000000000000..90a18b7efa14
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-1.1.0-test-readline.patch
@@ -0,0 +1,11 @@
+diff -Nur src.orig/configure src/configure
+--- src.orig/configure	2012-06-12 00:57:14.000000000 +0100
++++ src/configure	2012-06-12 18:19:56.000000000 +0100
+@@ -4598,6 +4598,7 @@
+ 		if test "$_readline" = yes || test "$_readline" = auto;
+ 		then
+ cat > $TMPC << EOF
++#include <stdio.h>
+ #include <readline/readline.h>
+ int main(void) { return 0; }
+ EOF
diff --git a/sci-libs/shogun/files/shogun-1.1.0-test-snappy.patch b/sci-libs/shogun/files/shogun-1.1.0-test-snappy.patch
new file mode 100644
index 000000000000..5d112d861b71
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-1.1.0-test-snappy.patch
@@ -0,0 +1,13 @@
+diff -Nur src.orig/configure src/configure
+--- src.orig/configure	2012-06-12 00:57:14.000000000 +0100
++++ src/configure	2012-06-12 18:03:33.000000000 +0100
+@@ -3512,7 +3512,8 @@
+ 	size_t input_length = (size_t) argc;
+ 	char* output = new char[snappy::MaxCompressedLength(input_length)];
+ 	size_t output_length;
+-	RawCompress(input, input_length, output, &output_length);
++	char *input;
++	snappy::RawCompress(input, input_length, output, &output_length);
+ 	delete [] output;
+ 	return int(output_length);
+ }
diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml
new file mode 100644
index 000000000000..72a2a3c06a1a
--- /dev/null
+++ b/sci-libs/shogun/metadata.xml
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+   SHOGUN - is a new machine learning toolbox with focus on large
+   scale kernel methods and especially on Support Vector Machines
+   (SVM) with focus to bioinformatics. It provides a generic SVM
+   object interfacing to several different SVM implementations. Each
+   of the SVMs can be combined with a variety of the many kernels
+   implemented. It can deal with weighted linear combination of a
+   number of sub-kernels, each of which not necessarily working on the
+   same domain, where  an optimal sub-kernel weighting can be learned
+   using Multiple Kernel Learning.  Apart from SVM 2-class
+   classification and regression problems, a number of linear methods
+   like Linear Discriminant Analysis (LDA), Linear Programming Machine
+   (LPM), (Kernel) Perceptrons and also algorithms to train hidden
+   markov models are implemented. The input feature-objects can be
+   dense, sparse or strings and of type int/short/double/char and can
+   be converted into different feature types. Chains of preprocessors
+   (e.g. substracting the mean) can be attached to each feature object
+   allowing for on-the-fly pre-processing.
+</longdescription>
+<use>
+  <flag name="arpack">Enable support for <pkg>sci-libs/arpack</pkg></flag>
+  <flag name="glpk">Enable support for <pkg>sci-mathematics/glpk</pkg></flag>
+  <flag name="json">Enable support for parsing JSON format</flag>
+  <flag name="lpsolve">Enable support for Linear Programming Solver</flag>
+  <flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag>
+  <flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag>
+  <flag name="snappy">Enable support for snappy compression</flag>
+  <flag name="superlu">Enable support for <pkg>sci-libs/superlu</pkg></flag>
+</use>
+</pkgmetadata>
diff --git a/sci-libs/shogun/shogun-1.1.0.ebuild b/sci-libs/shogun/shogun-1.1.0.ebuild
new file mode 100644
index 000000000000..1a99992e76dc
--- /dev/null
+++ b/sci-libs/shogun/shogun-1.1.0.ebuild
@@ -0,0 +1,157 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/shogun-1.1.0.ebuild,v 1.1 2012/06/14 17:16:03 bicatali Exp $
+
+EAPI=4
+
+inherit multilib versionator toolchain-funcs java-pkg-opt-2
+
+MYPV=$(get_version_component_range 1-2)
+MYPD=${PN}-data-0.3
+
+DESCRIPTION="Large Scale Machine Learning Toolbox"
+HOMEPAGE="http://shogun-toolbox.org/"
+SRC_URI="ftp://shogun-toolbox.org/shogun/releases/${MYPV}/sources/${P}.tar.bz2
+	test? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )"
+
+LICENSE="GPL-3 free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="arpack bzip2 doc examples glpk gzip hdf5 json lapack lpsolve mono lua lzma
+	lzo java R ruby	octave python readline snappy static-libs superlu test xml"
+
+RDEPEND="sci-libs/gsl
+	sys-libs/zlib
+	arpack? ( sci-libs/arpack )
+	bzip2? ( app-arch/bzip2 )
+	glpk? ( sci-mathematics/glpk )
+	gzip? ( app-arch/gzip )
+	hdf5? ( sci-libs/hdf5 )
+	java? ( >=virtual/jdk-1.5 )
+	json? ( dev-libs/json-c )
+	lapack? ( virtual/cblas virtual/lapack )
+	lpsolve? ( sci-mathematics/lpsolve )
+	lua? ( dev-lang/lua )
+	lzo? ( dev-libs/lzo )
+	mono? ( dev-lang/mono )
+	octave? ( sci-mathematics/octave[hdf5=] )
+	python? ( dev-python/numpy )
+	R? ( dev-lang/R )
+	readline? ( sys-libs/readline )
+	ruby? ( >=dev-ruby/narray-0.6.0.1-r2 )
+	snappy? ( app-arch/snappy )
+	superlu? ( sci-libs/superlu )
+	xml? ( dev-libs/libxml2 )"
+
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen[dot] )
+	java? ( dev-lang/swig dev-java/ant )
+	octave? ( dev-lang/swig )
+	python? ( dev-lang/swig test? ( sci-libs/scipy ) )
+	ruby? ( dev-lang/swig )"
+
+S="${WORKDIR}/${P}/src"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-respect-ldflags.patch \
+		"${FILESDIR}"/${P}-test-snappy.patch \
+		"${FILESDIR}"/${P}-test-readline.patch
+
+	# dist-packages is only for debian
+	# remove exagarated optimizations (-O9 does not exist...)
+	# use gentoo lapack framework
+	sed -i \
+		-e 's/dist-packages/site-packages/g' \
+		-e '/^COMP_OPTS=/d' \
+		-e "s/-llapack -lcblas/$(pkg-config --libs cblas lapack)/g" \
+		configure || die
+
+	# disable ldconfig which violates sandbox
+	# install in gentoo java standard paths
+	sed -i \
+		-e '/ldconfig/d' \
+		-e '/share\/java/d' \
+		-e '/jni/d' \
+		Makefile.template || die
+}
+
+src_configure() {
+	# define interfaces to shogun library to build
+	local x iface
+	for x in java lua octave python ruby ; do
+		use ${x} && iface="${iface}${x}_modular,"
+	done
+	use mono &&	iface="${iface}csharp_modular,"
+	use R && iface="${iface}r_modular,"
+	if use static-libs; then
+		iface="${iface}cmdline_static,"
+		use octave && iface="${iface}octave_static,"
+		use python && iface="${iface}python_static,"
+		use R && iface="${iface}r_static,"
+		use octave && use python && use R && iface="${iface}elwms_static,"
+	fi
+	iface="${iface%,}"
+
+	# gentoo bug #302621
+	use hdf5 && has_version sci-libs/hdf5[mpi] && export CXX=mpicxx CC=mpicc
+
+	./configure \
+		--disable-cpudetection \
+		--destdir="${ED}" \
+		--prefix="${EPREFIX}/usr" \
+		--mandir="${EPREFIX}/usr/share/man" \
+		--libdir="${EPREFIX}/usr/$(get_libdir)" \
+		--cc="$(tc-getCC)" \
+		--cxx="$(tc-getCXX)" \
+		--target="${CTARGET}" \
+		--interfaces=${iface} \
+		$(use_enable arpack) \
+		$(use_enable bzip2) \
+		$(use_enable doc doxygen) \
+		$(use_enable glpk) \
+		$(use_enable gzip) \
+		$(use_enable hdf5) \
+		$(use_enable json) \
+		$(use_enable lapack) \
+		$(use_enable lpsolve) \
+		$(use_enable lzma) \
+		$(use_enable lzo) \
+		$(use_enable readline) \
+		$(use_enable snappy) \
+		$(use_enable static-libs static) \
+		$(use_enable superlu) \
+		$(use_enable xml)
+}
+
+src_compile() {
+	emake
+	use doc && emake -C ../doc
+}
+
+src_test() {
+	use lapack || return
+	ln -s ../../${MYPD}/* ../data/
+	emake DESTDIR="${D}" install
+	# disable because very long and buggy dynamic paths (assumed install)
+	# emake tests
+	emake -C shogun check-examples
+}
+
+src_install() {
+	default
+	use static-libs || rm -f "${ED}"/usr/$(get_libdir)/*.a
+	if use java; then
+		java-pkg_dojar interfaces/java_modular/shogun.jar
+		java-pkg_doso interfaces/java_modular/libmodshogun.so
+	fi
+
+	use doc && dohtml -r ../doc/html/*
+	if use examples; then
+		insinto /usr/share/doc/${PF}
+		emake -C ../examples clean
+		doins -r ../examples
+		newins -r ../../${MYPD} data
+	fi
+}