commit: 8d85f22fd38976093c4b3d3a9f5d30954e689c14
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 4 21:02:10 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 4 21:07:06 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8d85f22f
sci-libs/shogun: Version bump to 5.0.0
Gentoo-bug: 550134, 570014, 587324, 593310,
602534, 604670, 606770, 607122
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3782
sci-libs/shogun/Manifest | 1 +
.../files/shogun-5.0.0-fix-buildsystem.patch | 72 ++++++++++
sci-libs/shogun/metadata.xml | 55 +++----
sci-libs/shogun/shogun-5.0.0.ebuild | 160 +++++++++++++++++++++
4 files changed, 261 insertions(+), 27 deletions(-)
diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
index 0469645..b92de5f 100644
--- a/sci-libs/shogun/Manifest
+++ b/sci-libs/shogun/Manifest
@@ -1,2 +1,3 @@
DIST shogun-4.1.0.tar.bz2 2908955 SHA256
0eb313a95606edee046768a4577d63f32f7ccce340bed7bf0ff0d69225567185 SHA512
01950d5186a94735df5331752e1b97a5464015973ddba38a70bc977f9872b3aad02b162ae87919631cce56d1f10b0bea1fa7b463bf959816e5a15a726214f52a
WHIRLPOOL
300bd0d887fe8ee4a1ac2aca7f3fbaebd4344dcffe2b20f9b5bb05e83d6973e8a98e54a216d99329c03eea2c02666c557a3c50ff7e11556298d119b8c262f762
+DIST shogun-5.0.0.tar.bz2 2448509 SHA256
e82c6a58db9db6624192b018750b0e41f793481791fdc9a6d328bf278d0ae70d SHA512
fa8d9dee4596acce12022540a6927cbdb62e08f8468c8be3790de07ebf3a53055032bcc532b28334ca83284c38f2b0153602634f12bafe4019acb9121b9ff236
WHIRLPOOL
532058c44680909f3717785035c13fb3cf48efec22924101975d80990cb2a9e151814c673ad1a03fa33e363abbaf21fc9edc99d7d25686cc67e907547217bf69
DIST shogun-data-0.9.tar.bz2 287533841 SHA256
691dd37ccc9bdd4f56d6b7a8e061e80567c241219d70210f8148bc4b7b815559 SHA512
ab501640e2db650603899c857866b451fac5c7bbbc7b4ef98559581928869cea49aa326dfca1bb398eee7ebc8843dcc8ee3105c9f462718f1af672aac6b9340a
WHIRLPOOL
19aa7a6d84be9ac7d8aaf7fb12747e17e0ba5a7ec8770b83cc1833b07cd1c6c397684a96eb8ebe709d544967ffaf23bcfbeea52dc8ddedf487fcf54a6d2b3ef7
diff --git a/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch
b/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch
new file mode 100644
index 00000000..1eb7cd0
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch
@@ -0,0 +1,72 @@
+* Remove setting of user flags
+* Remove erroneous bundling of Eigen
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -33,15 +33,6 @@
+ 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 ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-
+ # CCACHE
+ OPTION(ENABLE_CCACHE "Enable ccache for compilation" ON)
+ FIND_PACKAGE(CCache)
+@@ -174,24 +165,6 @@
+ SET(COMPILER_WARNINGS "-Wall -Wno-unused-parameter -Wformat
-Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated")
+ ENDIF()
+
+-IF(CMAKE_COMPILER_IS_GNUCXX)
+- SET(RELEASE_COMPILER_FLAGS "-fexpensive-optimizations
-frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2
-fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops")
+- IF (${MACHINE} MATCHES "x86_64" OR ${MACHINE} MATCHES "i686")
+- SET(RELEASE_COMPILER_FLAGS "${RELEASE_COMPILER_FLAGS}
-mfpmath=sse")
+- ENDIF()
+-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)
+ IF(NOT CMAKE_COMPILER_IS_GNUCXX)
+@@ -617,13 +590,6 @@
+ include(external/Eigen3)
+ LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR})
+ ELSE()
+- # eigen3 bug related to aliasing operators and self-storing.
+- # TODO put in proper reference and version from when this is fixed
+- IF(${EIGEN_VERSION} VERSION_GREATER 3.2.90)
+- MESSAGE(WARNING "The system Eigen3 version ${EIGEN_VERSION} is buggy,
manually bundling.")
+- include(external/Eigen3)
+- ENDIF()
+-
+ LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR})
+ ENDIF()
+
+@@ -957,11 +923,6 @@
+ # Respect system's or distribution's C[XX]FLAGS.
+ OPTION(SWIG_WITH_SYSTEM_CFLAGS "Enable system's C[XX]FLAGS for compilation of
swig-binaries" ON)
+
+-IF(NOT ("${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)
diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml
index fd2f5a4..88454ce 100644
--- a/sci-libs/shogun/metadata.xml
+++ b/sci-libs/shogun/metadata.xml
@@ -1,31 +1,32 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
<pkgmetadata>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <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="R">Enable support for <pkg>dev-lang/R</pkg></flag>
- <flag name="octave">Enable support for
<pkg>sci-mathematics/octave</pkg></flag>
- </use>
+ <maintainer type="project">
+ <email>[email protected]</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <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="R">Enable support for <pkg>dev-lang/R</pkg></flag>
+ <flag name="octave">Enable support for
<pkg>sci-mathematics/octave</pkg></flag>
+ <flag name="opencl">Enable support for building against
OpenCL</flag>
+ </use>
</pkgmetadata>
diff --git a/sci-libs/shogun/shogun-5.0.0.ebuild
b/sci-libs/shogun/shogun-5.0.0.ebuild
new file mode 100644
index 00000000..b3984db
--- /dev/null
+++ b/sci-libs/shogun/shogun-5.0.0.ebuild
@@ -0,0 +1,160 @@
+# Copyright 1999-2017 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="cpu_flags_x86_sse doc examples lua octave opencl python R ruby
static-libs test"
+
+REQUIRED_USE="
+ python? ( ${PYTHON_REQUIRED_USE} )
+ test? ( python )"
+
+RDEPEND="
+ app-arch/bzip2
+ app-arch/gzip
+ app-arch/lzma
+ app-arch/snappy
+ dev-libs/lzo
+ dev-cpp/eigen:3
+ dev-libs/json-c:=
+ dev-libs/libxml2
+ dev-libs/protobuf:=
+ net-misc/curl
+ sci-libs/arpack
+ sci-libs/arprec
+ sci-libs/colpack
+ sci-libs/hdf5:=
+ sci-libs/nlopt
+ sci-mathematics/glpk:=
+ sci-mathematics/lpsolve:=
+ sys-libs/readline:0=
+ sys-libs/zlib
+ virtual/blas
+ virtual/cblas
+ virtual/lapack
+ lua? ( dev-lang/lua:0 )
+ octave? ( >=sci-mathematics/octave-4.2.0:=[hdf5] )
+ opencl? ( virtual/opencl )
+ python? ( dev-python/numpy[${PYTHON_USEDEP}] )
+ R? ( dev-lang/R )
+ ruby? ( dev-ruby/narray )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig
+ doc? (
+ >=app-doc/doxygen-1.8.13-r1[dot]
+ dev-python/sphinx
+ )
+ lua? ( >=dev-lang/swig-3.0.12 )
+ octave? ( >=dev-lang/swig-3.0.12 )
+ python? (
+ >=dev-lang/swig-3.0.12
+ test? (
+ sci-libs/scipy
+ )
+ )
+ R? ( >=dev-lang/swig-3.0.12 )
+ ruby? ( >=dev-lang/swig-3.0.12 )
+ test? (
+ dev-python/jinja[${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=(
+ "${FILESDIR}"/${PN}-5.0.0-fix-buildsystem.patch
+ "${FILESDIR}"/${PN}-4.1.0-remove-C-linkage.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_RPATH=ON
+ -DCMAKE_SKIP_INSTALL_RPATH=ON
+ -DLIB_INSTALL_DIR=$(get_libdir)
+ -DENABLE_TESTING=$(usex test)
+ -DBUILD_EXAMPLES=$(usex examples)
+ -DDISABLE_SSE=$(usex !cpu_flags_x86_sse)
+ -DCMAKE_DISABLE_FIND_PACKAGE_Pandoc=ON
+ $(cmake-utils_use_find_package doc Sphinx)
+ $(cmake-utils_use_find_package doc Doxygen)
+
+ # Features:
+ -DENABLE_COVERAGE=OFF
+ -DENABLE_COLPACK=ON
+ -DENABLE_PROTOBUF=ON
+ -DENABLE_PYTHON_DEBUG=OFF
+ -DENABLE_VIENNACL=$(usex opencl)
+ -DUSE_ARPREC=ON
+ -DUSE_HDF5=ON
+
+ # Bindings:
+ -DJavaModular=OFF
+ -DPerlModular=OFF
+ -DCSharpModular=OFF
+ -DLuaModular=$(usex lua)
+ -DOctaveModular=$(usex octave)
+ -DPythonModular=$(usex python)
+ -DRModular=$(usex R)
+ -DRubyModular=$(usex ruby)
+
+ # Disable bundled libs
+ -DBUNDLE_COLPACK=OFF
+ -DBUNDLE_JSON=OFF
+ -DBUNDLE_NLOPT=OFF
+ )
+ 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 && cmake-utils_src_compile -C doc
+}
+
+src_install() {
+ cmake-utils_src_install
+
+ if use doc; then
+ local i
+ for i in lua octave python R ruby; do
+ if use $i; then
+ docinto html/${i,}_modular
+ dodoc -r
"${BUILD_DIR}"/src/interfaces/${i,}_modular/modshogun/doxygen_xml/.
+ fi
+ done
+ fi
+}
