From c66fb61dcab1be78b2c53225a30bb1b7f888b933 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sun, 25 Jan 2015 17:41:11 +0000 Subject: [PATCH] sci-libs/shogun: Fix buildproblems with atlas detection, #507304; be multilib friendly, #531034; do not fetch gmock for tests, #528566 Package-Manager: portage-2.2.15/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- sci-libs/shogun/ChangeLog | 9 ++++-- sci-libs/shogun/Manifest | 29 +++++++++++++++++-- .../shogun/files/shogun-3.2.0-atlas.patch | 22 ++++++++++++++ sci-libs/shogun/metadata.xml | 28 +++++++++--------- sci-libs/shogun/shogun-3.2.0.ebuild | 29 ++++++++++++++----- 5 files changed, 90 insertions(+), 27 deletions(-) create mode 100644 sci-libs/shogun/files/shogun-3.2.0-atlas.patch diff --git a/sci-libs/shogun/ChangeLog b/sci-libs/shogun/ChangeLog index a8873c3dac67..2d7f3bb7e15a 100644 --- a/sci-libs/shogun/ChangeLog +++ b/sci-libs/shogun/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-libs/shogun -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/ChangeLog,v 1.8 2014/04/06 01:47:16 bicatali Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/ChangeLog,v 1.9 2015/01/25 17:41:02 jlec Exp $ + + 25 Jan 2015; Justin Lecher shogun-3.2.0.ebuild, + +files/shogun-3.2.0-atlas.patch, metadata.xml: + Fix buildproblems with atlas detection, #507304; be multilib friendly, + #531034; do not fetch gmock for tests, #528566 *shogun-3.2.0 (06 Apr 2014) diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest index 4e9ae6295dcb..8e8f08fc0078 100644 --- a/sci-libs/shogun/Manifest +++ b/sci-libs/shogun/Manifest @@ -1,7 +1,11 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA512 + AUX shogun-1.1.0-as-needed.patch 2137 SHA256 de8bb8e6f42873b0fbc3c4f816869684b93d0ecceb6ea6db7c77e9e86bf79617 SHA512 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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 index 70e3e2616088..d0c30a0c09fb 100644 --- a/sci-libs/shogun/metadata.xml +++ b/sci-libs/shogun/metadata.xml @@ -1,8 +1,8 @@ -sci - + sci + 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 @@ -21,17 +21,17 @@ (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. - - Enable support for sci-libs/arpack - Enable support for matrix package dev-cpp/eigen - Enable support for sci-mathematics/glpk - Enable support for parsing JSON format - Enable support for Linear Programming Solver - Enable support non linear optimization from + + Enable support for sci-libs/arpack + Enable support for matrix package dev-cpp/eigen + Enable support for sci-mathematics/glpk + Enable support for parsing JSON format + Enable support for Linear Programming Solver + Enable support non linear optimization from sci-libs/nlopt - Enable support for dev-lang/R - Enable support for sci-mathematics/octave - Enable support for snappy compression - Enable support for sci-libs/superlu - + Enable support for dev-lang/R + Enable support for sci-mathematics/octave + Enable support for snappy compression + Enable support for sci-libs/superlu + diff --git a/sci-libs/shogun/shogun-3.2.0.ebuild b/sci-libs/shogun/shogun-3.2.0.ebuild index e7e0b4d95702..4bce5a8850a0 100644 --- a/sci-libs/shogun/shogun-3.2.0.ebuild +++ b/sci-libs/shogun/shogun-3.2.0.ebuild @@ -1,27 +1,32 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/shogun-3.2.0.ebuild,v 1.1 2014/04/06 01:47:16 bicatali Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/shogun-3.2.0.ebuild,v 1.2 2015/01/25 17:41:02 jlec Exp $ EAPI=5 -PYTHON_COMPAT=( python{2_7,3_3} ) -inherit cmake-utils multilib versionator toolchain-funcs python-single-r1 +PYTHON_COMPAT=( python2_7 python{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 +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} )" + +REQUIRED_USE=" + python? ( ${PYTHON_REQUIRED_USE} ) + test? ( python ) + " RDEPEND=" app-arch/bzip2:= @@ -62,13 +67,20 @@ DEPEND="${RDEPEND} 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 )" + 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}"/${P}-atlas.patch +) + pkg_setup() { use python && python-single-r1_pkg_setup } @@ -88,6 +100,7 @@ src_configure() { -DENABLE_COVERAGE=OFF -DJavaModular=OFF -DPerlModular=OFF + -DLIB_INSTALL_DIR=$(get_libdir) $(cmake-utils_use lua LuaModular) $(cmake-utils_use mono CSharpModular) $(cmake-utils_use octave OctaveModular) -- 2.26.2