proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

10 files changed, 610 insertions, 0 deletions

diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
new file mode 100644
index 00000000000..11c82bf05c0
--- /dev/null
+++ b/sci-libs/shogun/Manifest
@@ -0,0 +1,6 @@
+DIST shogun-1.1.0.tar.bz2 3485714 SHA256 9f69638f0bc18995358c38cd6eed6437e6b90c1fceab7c6e64c9739b7e6cc40b SHA512 853168e3d68ad02ef543391b78c51682d004af46acddfa09a76b41e373e27199fc9be0598892207e116a82f24437e3f1c0dc97c3e28ca32879594fbe112bd157 WHIRLPOOL dd044ff2cc9fd9376b80f1efd9bbcf901b11765a2f85eb2325ddd640ea547e513df8c9da548634e49758ef124147666f86b6b4082e118c6d35ef2d5010527cf9
+DIST shogun-2.0.0.tar.bz2 4106437 SHA256 b18e30515b9f4432d02602d0dd66dbc57c70a46f71636275071afaee94e245ee SHA512 e7c8d515afbcb3198aade32d2962e8d94b669b9c79ddbcd7425f04bbb0379803f7353c50ba8897356842cddb401d303fefaf8a7f9dd6a2e751e176deba1e46f1 WHIRLPOOL aa9ef89f28acc012ee2894c4ff6858f7bf01585d02160d5b2df33159c7c87593ea352833765a7a78cc0ed16fd10713d285eb711606f0e3771ec685778f703570
+DIST shogun-3.2.0.tar.bz2 4217245 SHA256 bc416b615ed90aef80c58a30546c5e2da779347bebb8742ecf11657073fc8f72 SHA512 7c420da7bf10c8971954964bce4dc13a8f64c6ff2a0976293f54947414ad2fe7171b1747cef3e2ceb969cf936d8fe862e940582f642cd2367897cda3191b186b WHIRLPOOL bce007c01ebee0e225d5cf858e042561a540416b349015ac566cce82b77096e8206b2f9e51572d9ee8149651a39aa30d6438b28d37ba43eb5aba593b10c5e497
+DIST shogun-data-0.3.tar.bz2 126676026 SHA256 34272e3f5e6b6989a4941b925ab3a9cd1525d73180681884e948a673aff4ef89 SHA512 92c7e7dae1df5a7a79428a7f2116b1d9d825a37d4145edfdff1fb7b707853eab19ffe848c4ae2bc2338a93373e78c7cae4087df260411a9576b031e7a6f0de95 WHIRLPOOL 24987580c967b05e61ee5402fe30701cabe17d7ffb29b4966ff0abd0d03e197b928f018e617e254395c6939f93de3e397f5ce7df7c3d4ae7dfe4e782c345fe85
+DIST shogun-data-0.4.tar.bz2 127377123 SHA256 103ef944c7211f64957833cd6ace85e32629d73ef286273424e239fa454ecfcc SHA512 c178f6d5d8e4b6b6a94b74da5c133b01e83a1d4c7bf5d0fd66b4812b259934dbc998cfc1ef64f19b17b5099e8c389b8e359e69f1cc1bef6b82b940dc97cac46d WHIRLPOOL cef5d84f342523bad8b810fa3018669e9cd838c7c45bb37b8e7308dce448dc9b98f9aa6716aa724d64746539ef9c041a71cd2f3a1af71ed1077d276a192573d5
+DIST shogun-data-0.8.tar.bz2 261905079 SHA256 a2a0c8ccd754f0b893d97d77cfb60e25fcdb4e7033731434fb07e5483514a047 SHA512 9ea48706aae5ca116e8cf3507d1fcd06e24a8384abe6f2ebaf3c81735237d3beceee26ce5af97b85af24409eb47da684f7e7a56c0800a82c40ed214e6382978f WHIRLPOOL 3a3120a8e982c90c670ec0c206635abdcb152ae5f312172ec58ae21e1ee11f15c406b382bd3b8e8a63300302290590b83a977bd4d90375160ceb8ae516409c12
diff --git a/sci-libs/shogun/files/shogun-1.1.0-as-needed.patch b/sci-libs/shogun/files/shogun-1.1.0-as-needed.patch
new file mode 100644
index 00000000000..5d365472c2c
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-1.1.0-as-needed.patch
@@ -0,0 +1,48 @@
+diff -Nur src.orig/configure src/configure
+--- src.orig/configure	2012-08-04 12:58:58.230092977 -0700
++++ src/configure	2012-08-04 13:30:14.441859756 -0700
+@@ -4470,7 +4470,8 @@
+ 				COMPFLAGS_C_R="$COMPFLAGS_C_R `R CMD config CPICFLAGS`"
+ 				COMPFLAGS_CPP_R="$COMPFLAGS_CPP_R `R CMD config CXXPICFLAGS`"
+ 				INCLUDES_R="$INCLUDES_R `R CMD config --cppflags`"
+-				LINKFLAGS_R="$LINKFLAGS_R `R CMD config --ldflags` `R CMD config DYLIB_LDFLAGS`"
++				PRELINKFLAGS_R="$PRELINKFLAGS_R `R CMD config DYLIB_LDFLAGS`"
++				LINKFLAGS_R="$LINKFLAGS_R `R CMD config --ldflags`"
+ 			fi
+ 
+ 
+diff -Nur src.orig/Makefile.template src/Makefile.template
+--- src.orig/Makefile.template	2012-08-04 12:58:58.229092986 -0700
++++ src/Makefile.template	2012-08-04 13:00:21.340525955 -0700
+@@ -515,7 +515,7 @@
+ else
+ $(TEMPLATE_TARGET): .depend $(OBJFILES) $(SRCFILES) $(HEADERFILES) $(OTHERDEPS)
+ 	$(LINK) $(PRELINKFLAGS) $(shell find $(SRCDIR) -name "*.$(EXT_OBJ_CPP)" -o \
+-		-name "*.$(EXT_OBJ_C)" 2>/dev/null) $(LINKFLAGS) -o $@ $(POSTLINKFLAGS)
++		-name "*.$(EXT_OBJ_C)" 2>/dev/null) $(LINKFLAGS) $(POSTLINKFLAGS) -o $@
+ 	@$(POSTLINKCMD) $@
+ 	@$(LIBSYMLINKCMD)
+ endif
+@@ -530,18 +530,18 @@
+ 		($(LIBRARY_PATH)=$(CONFIGPATH)/../shogun R --no-save)
+ 
+ $(PRE_LIB_SWIG_TEMPLATE)%${EXT_LIB_SWIG_TEMPLATE}:	%$(EXT_OBJ_SWIG)
+-	$(LINK) $(LINKFLAGS) -o $@ $^ $(POSTLINKFLAGS)
++	$(LINK) $(LINKFLAGS) $^ $(POSTLINKFLAGS) -o $@
+ 
+ %${EXT_OBJ_SWIG}:	%$(EXT_SRC_SWIG)
+-	$(COMP_CPP) $(COMPFLAGS_SWIG_CPP) $(DEFINES) -c $(INCLUDES) -o $@ $<
++	$(COMP_CPP) $(COMPFLAGS_SWIG_CPP) $(DEFINES) -c $(INCLUDES) $< -o $@
+ 
+ %.$(EXT_OBJ_CPP):	%.$(EXT_SRC_CPP)
+-	$(COMP_CPP) $(COMPFLAGS_CPP) $(DEFINES) -c $(INCLUDES) -o $@ $<
++	$(COMP_CPP) $(COMPFLAGS_CPP) $(DEFINES) -c $(INCLUDES) $< -o $@
+ 	@test -f $*.$(EXT_CPP_TMP) && test "$(SRCDIR)" != "." \
+ 	  && rm -f $< || true
+ 
+ %.$(EXT_OBJ_C):	%.$(EXT_SRC_C)
+-	$(COMP_C) $(COMPFLAGS_C) $(DEFINES) -c $(INCLUDES) -o $@ $<
++	$(COMP_C) $(COMPFLAGS_C) $(DEFINES) -c $(INCLUDES) $< -o $@
+ 
+ %.$(EXT_SRC_CPP): %.$(EXT_CPP_TMP) %.$(EXT_CPP_SH) $(HEADERFILES)
+ 	@echo "generating $@ from $*.$(EXT_CPP_TMP) by running $*.$(EXT_CPP_SH)"
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 00000000000..60753606cdb
--- /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="$LDFLAGS -lpthread"
+ POSTLINKFLAGS=
+ 
+ INCLUDES_STATIC_INTERFACES=
diff --git a/sci-libs/shogun/files/shogun-1.1.0-test-readline.patch b/sci-libs/shogun/files/shogun-1.1.0-test-readline.patch
new file mode 100644
index 00000000000..90a18b7efa1
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-1.1.0-test-readline.patch
@@ -0,0 +1,11 @@
+diff -Nur src.orig/configure src/configure
+--- src.orig/configure	2012-06-12 00:57:14.000000000 +0100
++++ src/configure	2012-06-12 18:19:56.000000000 +0100
+@@ -4598,6 +4598,7 @@
+ 		if test "$_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 00000000000..5d112d861b7
--- /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/files/shogun-3.2.0-atlas.patch b/sci-libs/shogun/files/shogun-3.2.0-atlas.patch
new file mode 100644
index 00000000000..a4f5e1c77d7
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-3.2.0-atlas.patch
@@ -0,0 +1,22 @@
+ cmake/FindAtlas.cmake | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/cmake/FindAtlas.cmake b/cmake/FindAtlas.cmake
+index 13f092d..8c2dd2f 100644
+--- a/cmake/FindAtlas.cmake
++++ b/cmake/FindAtlas.cmake
+@@ -20,10 +20,10 @@ if(ATLAS_LAPACK)
+   endif()
+   unset(CMAKE_REQUIRED_LIBRARIES CACHE)
+ else()
+-  find_file(ATLAS_LAPACK liblapack.so.3 PATHS /usr/lib/atlas /usr/lib64/atlas)
+-  find_library(ATLAS_LAPACK NAMES lapack)
+-  set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES} ${ATLAS_CBLAS})
+-  check_library_exists("${ATLAS_LAPACK}" clapack_dpotrf "" FOUND_CLAPACK)
++  # find_file(ATLAS_LAPACK liblapack.so.3 PATHS /usr/lib/atlas /usr/lib64/atlas)
++  # find_library(ATLAS_LAPACK NAMES lapack)
++  # set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES} ${ATLAS_CBLAS})
++  check_library_exists("${ATLAS_LIBRARIES}" clapack_dpotrf "" FOUND_CLAPACK)
+   if(NOT FOUND_CLAPACK)
+     unset(ATLAS_LAPACK CACHE)
+   endif()
diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml
new file mode 100644
index 00000000000..d0c30a0c09f
--- /dev/null
+++ b/sci-libs/shogun/metadata.xml
@@ -0,0 +1,37 @@
+<?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="eigen">Enable support for matrix package <pkg>dev-cpp/eigen</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="nlopt">Enable support non linear optimization from
+  <pkg>sci-libs/nlopt</pkg></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 00000000000..477d86067fb
--- /dev/null
+++ b/sci-libs/shogun/shogun-1.1.0.ebuild
@@ -0,0 +1,160 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils 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/${MYPD}.tar.bz2 )
+	examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )"
+
+LICENSE="GPL-3 free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+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}"/${P}-test-readline.patch \
+		"${FILESDIR}"/${P}-as-needed.patch
+
+	# dist-packages is only for debian
+	# remove exagarated optimizations (-O9 does not exist...)
+	# use gentoo lapack framework
+	sed -i \
+		-e 's/dist-packages/site-packages/g' \
+		-e '/^COMP_OPTS=/d' \
+		-e "s:-llapack -lcblas:$($(tc-getPKG_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) \
+		$(use_enable xml) || die
+}
+
+src_compile() {
+	emake
+	use doc && emake -C ../doc
+}
+
+src_test() {
+	use lapack || return
+	ln -s ../../${MYPD}/* ../data/
+	emake DESTDIR="${ED}" install
+	# disable because very long and buggy dynamic paths (assumed install)
+	# emake tests
+	emake -C shogun check-examples
+}
+
+src_install() {
+	default
+	use static-libs || rm -f "${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
+		insinto /usr/share/doc/${PF}/data
+		doins -r "${WORKDIR}"/${MYPD}/*
+	fi
+}
diff --git a/sci-libs/shogun/shogun-2.0.0.ebuild b/sci-libs/shogun/shogun-2.0.0.ebuild
new file mode 100644
index 00000000000..8e26b7fb77e
--- /dev/null
+++ b/sci-libs/shogun/shogun-2.0.0.ebuild
@@ -0,0 +1,164 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils multilib versionator toolchain-funcs java-pkg-opt-2
+
+MYPV=$(get_version_component_range 1-2)
+MYPD=${PN}-data-0.4
+
+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/${MYPD}.tar.bz2 )
+	examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )"
+
+LICENSE="GPL-3 free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack bzip2 doc eigen examples glpk gzip hdf5 json lapack lpsolve mono lua lzma
+	lzo nlopt java R ruby octave python readline smp snappy static-libs superlu test xml"
+
+RDEPEND="
+	sci-libs/gsl
+	sys-libs/zlib
+	arpack? ( sci-libs/arpack )
+	bzip2? ( app-arch/bzip2 )
+	eigen? ( >=dev-cpp/eigen-3 )
+	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 )
+	nlopt? ( sci-libs/nlopt )
+	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="${RDEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen[dot] )
+	java? ( >=dev-lang/swig-2.0.4 dev-java/ant )
+	octave? ( >=dev-lang/swig-2.0.4 )
+	python? ( >=dev-lang/swig-2.0.4 test? ( sci-libs/scipy ) )
+	ruby? ( >=dev-lang/swig-2.0.4 )"
+
+S="${WORKDIR}/${P}/src"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-1.1.0-respect-ldflags.patch \
+		"${FILESDIR}"/${PN}-1.1.0-test-readline.patch \
+		"${FILESDIR}"/${PN}-1.1.0-as-needed.patch
+
+	# dist-packages is only for debian
+	# remove exagarated optimizations (-O9 does not exist...)
+	# use gentoo lapack framework
+	sed -i \
+		-e 's/dist-packages/site-packages/g' \
+		-e '/^COMP_OPTS=/d' \
+		-e "s:-llapack -lcblas:$($(tc-getPKG_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' \
+		-e 's/OCTAVE_LOADPATH/OCTAVE_PATH/g' \
+		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="${iface%,}"
+
+	# gentoo bug #302621
+	use hdf5 && has_version sci-libs/hdf5[mpi] && export CXX=mpicxx CC=mpicc
+	./configure \
+		--disable-cpudetection \
+		--destdir="${D}" \
+		--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 eigen eigen3) \
+		$(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 nlopt) \
+		$(use_enable readline) \
+		$(use_enable smp hmm-parallel) \
+		$(use_enable snappy) \
+		$(use_enable static-libs static) \
+		$(use_enable superlu) \
+		$(use_enable xml) || die
+}
+
+src_compile() {
+	emake
+	use doc && emake -C ../doc
+}
+
+src_test() {
+	use lapack || return
+	ln -s ../../${MYPD}/* ../data/
+	emake DESTDIR="${D}" install
+	# disable because very long
+	# emake tests
+	emake -C shogun check-examples
+}
+
+src_install() {
+	default
+	use static-libs || rm "${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
+		insinto /usr/share/doc/${PF}/data
+		doins -r "${WORKDIR}"/${MYPD}/*
+	fi
+}
diff --git a/sci-libs/shogun/shogun-3.2.0.ebuild b/sci-libs/shogun/shogun-3.2.0.ebuild
new file mode 100644
index 00000000000..51cfb508525
--- /dev/null
+++ b/sci-libs/shogun/shogun-3.2.0.ebuild
@@ -0,0 +1,137 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+inherit cmake-utils multilib python-single-r1 toolchain-funcs versionator
+
+MYPV=$(get_version_component_range 1-2)
+MYPD=${PN}-data-0.8
+
+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/${MYPD}.tar.bz2 )
+	examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )"
+
+LICENSE="GPL-3 free-noncomm"
+SLOT="0/16"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc examples lua mono octave python R ruby static-libs test"
+
+REQUIRED_USE="
+	python? ( ${PYTHON_REQUIRED_USE} )
+	test? ( python )
+	"
+
+RDEPEND="
+	app-arch/bzip2:=
+	app-arch/gzip:=
+	app-arch/lzma:=
+	app-arch/snappy:=
+	dev-libs/lzo:=
+	>=dev-cpp/eigen-3.1
+	dev-libs/json-c:=
+	dev-libs/libxml2:=
+	dev-libs/protobuf:=
+	net-misc/curl:=
+	sci-libs/arpack:=
+	sci-libs/arprec:=
+	sci-libs/colpack:=
+	sci-libs/hdf5:=
+	sci-libs/nlopt:=
+	sci-mathematics/glpk:=
+	sci-mathematics/lpsolve:=
+	sys-libs/readline
+	sys-libs/zlib:=
+	virtual/blas
+	virtual/cblas
+	virtual/lapack
+	lua? ( dev-lang/lua )
+	mono? ( dev-lang/mono )
+	octave? ( sci-mathematics/octave[hdf5] )
+	python? ( dev-python/numpy[${PYTHON_USEDEP}] )
+	R? ( dev-lang/R )
+	ruby? ( dev-ruby/narray )"
+
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen[dot] )
+	lua? ( >=dev-lang/swig-2.0.4 )
+	mono? ( >=dev-lang/swig-2.0.4 )
+	octave? ( >=dev-lang/swig-2.0.4 )
+	python? ( >=dev-lang/swig-2.0.4 test? ( sci-libs/scipy ) )
+	R? ( >=dev-lang/swig-2.0.4 )
+	ruby? ( >=dev-lang/swig-2.0.4 )
+	test? (
+		dev-python/jinja[${PYTHON_USEDEP}]
+		dev-cpp/gmock
+		)"
+
+# javamodular needs jblas (painful to package properly)
+# permodular work in progress (as 3.2.0)
+# could actually support multiple pythons, multiple rubys
+# feel free to do work for it
+
+PATCHES=(
+	"${FILESDIR}"/${P}-atlas.patch
+)
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+}
+
+src_configure() {
+	export ATLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas lapack)"
+	export CBLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas)"
+	export ATLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas cblas lapack)"
+	export LAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+	local mycmakeargs=(
+		-DBUILD_EXAMPLES=OFF
+		-DBUNDLE_ARPREC=OFF
+		-DBUNDLE_COLPACK=OFF
+		-DBUNDLE_EIGEN=OFF
+		-DBUNDLE_JSON=OFF
+		-DBUNDLE_NLOPT=OFF
+		-DENABLE_COVERAGE=OFF
+		-DJavaModular=OFF
+		-DPerlModular=OFF
+		-DLIB_INSTALL_DIR=$(get_libdir)
+		$(cmake-utils_use lua LuaModular)
+		$(cmake-utils_use mono CSharpModular)
+		$(cmake-utils_use octave OctaveModular)
+		$(cmake-utils_use octave OctaveStatic)
+		$(cmake-utils_use python PythonModular)
+		$(cmake-utils_use python PythonStatic)
+		$(cmake-utils_use R RModular)
+		$(cmake-utils_use R RStatic)
+		$(cmake-utils_use ruby RubyModular)
+		$(cmake-utils_use test ENABLE_TESTING)
+	)
+	cmake-utils_src_configure
+	# gentoo bug #302621
+	has_version sci-libs/hdf5[mpi] && export CXX=mpicxx CC=mpicc
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	use doc && emake -C doc
+}
+
+src_install() {
+	cmake-utils_src_install
+	use doc && dohtml -r doc/html/*
+	if use examples; then
+		insinto /usr/share/doc/${PF}
+		emake -C examples clean
+		doins -r examples
+		docompress -x /usr/share/doc/${PF}/examples
+		insinto /usr/share/doc/${PF}/data
+		doins -r "${WORKDIR}"/${MYPD}/*
+
+	fi
+}