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authorRobin H. Johnson <robbat2@gentoo.org>2015-08-08 13:49:04 -0700
committerRobin H. Johnson <robbat2@gentoo.org>2015-08-08 17:38:18 -0700
commit56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-libs/shogun
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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
Diffstat (limited to 'sci-libs/shogun')
-rw-r--r--sci-libs/shogun/Manifest6
-rw-r--r--sci-libs/shogun/files/shogun-1.1.0-as-needed.patch48
-rw-r--r--sci-libs/shogun/files/shogun-1.1.0-respect-ldflags.patch12
-rw-r--r--sci-libs/shogun/files/shogun-1.1.0-test-readline.patch11
-rw-r--r--sci-libs/shogun/files/shogun-1.1.0-test-snappy.patch13
-rw-r--r--sci-libs/shogun/files/shogun-3.2.0-atlas.patch22
-rw-r--r--sci-libs/shogun/metadata.xml37
-rw-r--r--sci-libs/shogun/shogun-1.1.0.ebuild160
-rw-r--r--sci-libs/shogun/shogun-2.0.0.ebuild164
-rw-r--r--sci-libs/shogun/shogun-3.2.0.ebuild137
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
+}