commit: 4fada4576c7247539d4fd77238ad1c8e3a410620
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat May 7 16:32:50 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat May 7 16:38:01 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4fada457
sci-libs/shogun: Version bump to latest 4.1.0 release
Package-Manager: portage-2.2.28
sci-libs/shogun/Manifest | 2 +
.../files/shogun-4.1.0-fix-buildsystem.patch | 81 +++++++++++++
sci-libs/shogun/shogun-4.1.0.ebuild | 127 +++++++++++++++++++++
3 files changed, 210 insertions(+)
diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
index 11c82bf..2cb0ed7 100644
--- a/sci-libs/shogun/Manifest
+++ b/sci-libs/shogun/Manifest
@@ -1,6 +1,8 @@
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-4.1.0.tar.bz2 2908955 SHA256
0eb313a95606edee046768a4577d63f32f7ccce340bed7bf0ff0d69225567185 SHA512
01950d5186a94735df5331752e1b97a5464015973ddba38a70bc977f9872b3aad02b162ae87919631cce56d1f10b0bea1fa7b463bf959816e5a15a726214f52a
WHIRLPOOL
300bd0d887fe8ee4a1ac2aca7f3fbaebd4344dcffe2b20f9b5bb05e83d6973e8a98e54a216d99329c03eea2c02666c557a3c50ff7e11556298d119b8c262f762
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
+DIST shogun-data-0.9.tar.bz2 287533841 SHA256
691dd37ccc9bdd4f56d6b7a8e061e80567c241219d70210f8148bc4b7b815559 SHA512
ab501640e2db650603899c857866b451fac5c7bbbc7b4ef98559581928869cea49aa326dfca1bb398eee7ebc8843dcc8ee3105c9f462718f1af672aac6b9340a
WHIRLPOOL
19aa7a6d84be9ac7d8aaf7fb12747e17e0ba5a7ec8770b83cc1833b07cd1c6c397684a96eb8ebe709d544967ffaf23bcfbeea52dc8ddedf487fcf54a6d2b3ef7
diff --git a/sci-libs/shogun/files/shogun-4.1.0-fix-buildsystem.patch
b/sci-libs/shogun/files/shogun-4.1.0-fix-buildsystem.patch
new file mode 100644
index 0000000..e244c94
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-4.1.0-fix-buildsystem.patch
@@ -0,0 +1,81 @@
+Remove CFLAGS/CXXFLAGS setting which is not desired in Gentoo
+
+--- shogun-4.1.0/cmake/FindAtlas.cmake
++++ shogun-4.1.0/cmake/FindAtlas.cmake
+@@ -20,10 +20,10 @@
+ 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()
+--- shogun-4.1.0/CMakeLists.txt
++++ shogun-4.1.0/CMakeLists.txt
+@@ -23,15 +23,6 @@
+ SET(EIGEN_VERSION_MINIMUM 3.1.2)
+ SET(VIENNACL_VERSION_MINIMUM 1.5.0)
+
+-# Store system's or distribution's C[XX]FLAGS.
+-SET(SYSTEM_C_FLAGS "${CMAKE_C_FLAGS}")
+-SET(SYSTEM_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+-STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE_UC)
+-IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+- SET(CMAKE_C_FLAGS "")
+- SET(CMAKE_CXX_FLAGS "")
+-ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-
+ # CCACHE
+ OPTION(ENABLE_CCACHE "Enable ccache for compilation" ON)
+ FIND_PACKAGE(CCache)
+@@ -145,20 +136,8 @@
+ SET(COMPILER_WARNINGS "-Wall -Wno-unused-parameter -Wformat
-Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated")
+ ENDIF()
+
+-IF(CMAKE_COMPILER_IS_GNUCXX)
+- SET(RELEASE_COMPILER_FLAGS "-fexpensive-optimizations
-frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2
-fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops -mfpmath=sse")
+-ELSEIF("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+- SET(RELEASE_COMPILER_FLAGS "-funroll-loops")
+-ENDIF()
+-SET(SWIG_CXX_COMPILER_FLAGS "-O0 -g")
+ SET(CMAKE_C_FLAGS "${COMPILER_WARNINGS} ${CMAKE_C_FLAGS}")
+ SET(CMAKE_CXX_FLAGS "${COMPILER_WARNINGS} ${CMAKE_CXX_FLAGS}")
+-SET(CMAKE_C_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
+-SET(CMAKE_CXX_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
+-SET(CMAKE_C_FLAGS_DISTRIBUTION "-O2")
+-SET(CMAKE_CXX_FLAGS_DISTRIBUTION "-O2")
+-SET(CMAKE_C_FLAGS_DEBUG "-g")
+-SET(CMAKE_CXX_FLAGS_DEBUG "-g")
+
+ OPTION(ENABLE_COVERAGE "Enable code coverage" OFF)
+ IF(ENABLE_COVERAGE)
+@@ -881,21 +860,7 @@
+ OPTION(USE_SWIG_DIRECTORS "Enable SWIG director classes" OFF)
+
+ # Respect system's or distribution's C[XX]FLAGS.
+-OPTION(SWIG_WITH_SYSTEM_CFLAGS "Enable system's C[XX]FLAGS for compilation of
swig-binaries" ON)
+-
+-IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${SYSTEM_C_FLAGS}")
+- SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SYSTEM_CXX_FLAGS}")
+-ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-
+-IF(SWIG_WITH_SYSTEM_CFLAGS)
+- SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS}
${SYSTEM_CXX_FLAGS}")
+-ENDIF(SWIG_WITH_SYSTEM_CFLAGS)
+-
+-OPTION(REDUCE_SWIG_DEBUG "Reduce debuginfo when compiling interfaces" OFF)
+-IF(REDUCE_SWIG_DEBUG)
+- SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS} -g1")
+-ENDIF(REDUCE_SWIG_DEBUG)
++SET(SWIG_CXX_COMPILER_FLAGS "${CMAKE_CXX_FLAGS}")
+
+ # python modular
+ IF (PythonModular OR PythonStatic)
diff --git a/sci-libs/shogun/shogun-4.1.0.ebuild
b/sci-libs/shogun/shogun-4.1.0.ebuild
new file mode 100644
index 0000000..651f7bb
--- /dev/null
+++ b/sci-libs/shogun/shogun-4.1.0.ebuild
@@ -0,0 +1,127 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5} )
+
+inherit cmake-utils flag-o-matic python-single-r1 toolchain-funcs versionator
+
+MYPV=$(get_version_component_range 1-2)
+MYPD=${PN}-data-0.9
+
+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? ( ${PYTHON_REQUIRED_USE} )
+ test? ( python )"
+
+RDEPEND="
+ app-arch/bzip2:=
+ app-arch/gzip:=
+ app-arch/lzma:=
+ app-arch/snappy:=
+ dev-libs/lzo:=
+ >=dev-cpp/eigen-3.1
+ dev-libs/json-c:=
+ dev-libs/libxml2:=
+ dev-libs/protobuf:=
+ net-misc/curl:=
+ sci-libs/arpack:=
+ sci-libs/arprec:=
+ sci-libs/colpack:=
+ sci-libs/hdf5:=
+ sci-libs/nlopt:=
+ sci-mathematics/glpk:=
+ sci-mathematics/lpsolve:=
+ sys-libs/readline:0
+ sys-libs/zlib:=
+ virtual/blas
+ virtual/cblas
+ virtual/lapack
+ lua? ( dev-lang/lua:0 )
+ mono? ( dev-lang/mono )
+ octave? ( <sci-mathematics/octave-3.8.0[hdf5] )
+ python? ( dev-python/numpy[${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}-fix-buildsystem.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)"
+
+ append-cppflags "$($(tc-getPKG_CONFIG) --cflags cblas)"
+
+ local mycmakeargs=(
+ -DCMAKE_SKIP_INSTALL_RPATH=ON
+ -DCMAKE_SKIP_RPATH=ON
+ -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=$(get_libdir)
+ -DLuaModular="$(usex lua)"
+ -DCSharpModular="$(usex mono)"
+ -DOctaveModular="$(usex octave)"
+ -DOctaveStatic="$(usex octave)"
+ -DPythonModular="$(usex python)"
+ -DPythonStatic="$(usex python)"
+ -DRModular="$(usex R)"
+ -DRStatic="$(usex R)"
+ -DRubyModular="$(usex ruby)"
+ -DENABLE_TESTING="$(usex test)"
+ -DBUILD_EXAMPLES="$(usex examples)"
+ )
+ 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
+}
