[gentoo-commits] repo/gentoo:master commit in: sci-libs/shogun/, sci-libs/shogun/files/, profiles/

["Michał Górny" <mgorny@gentoo.org>]

commit:     524551cf255750e37c074627fe801b0d21512228
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 25 14:49:59 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Oct 25 14:50:26 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=524551cf

sci-libs/shogun: Remove last-rited pkg

Closes: https://bugs.gentoo.org/737412
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 profiles/package.mask                              |   6 -
 sci-libs/shogun/Manifest                           |   2 -
 .../files/shogun-4.1.0-remove-C-linkage.patch      |  24 ---
 .../files/shogun-5.0.0-fix-buildsystem.patch       |  72 ---------
 sci-libs/shogun/metadata.xml                       |  32 ----
 sci-libs/shogun/shogun-5.0.0-r1.ebuild             | 167 ---------------------
 6 files changed, 303 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index e5dc1cdd1a7..6599f3e8381 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -252,12 +252,6 @@ sys-apps/lcdtest
 =dev-python/pypy3-exe-7.3.2_p37*
 =dev-python/pypy3-exe-bin-7.3.2_p37*
 
-# Michał Górny <mgorny@gentoo.org> (2020-09-25)
-# Effectively unmaintained.  Not ported to py3.7.  Multiple unresolved
-# build failures reported.  No reverse dependencies.
-# Removal in 30 days.  Bug #737412.
-sci-libs/shogun
-
 # Michał Górny <mgorny@gentoo.org> (2020-09-09)
 # These packages (or package versions) still require Python 2.7.
 # They are either dead upstream, their Python 3 porting efforts are

diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
deleted file mode 100644
index 8a9281c8d29..00000000000
--- a/sci-libs/shogun/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST shogun-5.0.0.tar.bz2 2448509 BLAKE2B 85352d782740b4c671bb6081e0445bb7e801e27e36fdc0f82658b937fd6658c41016e4a91841ddb09ae9062b77d32f290f56b191318c1c34bf0812d1b9a8b364 SHA512 fa8d9dee4596acce12022540a6927cbdb62e08f8468c8be3790de07ebf3a53055032bcc532b28334ca83284c38f2b0153602634f12bafe4019acb9121b9ff236
-DIST shogun-data-0.9.tar.bz2 287533841 BLAKE2B 796830262205961b88715f4eb60a47ff2ad108426b7af8e4e1a0733920962ad8154a1ab9892356e9793be24d415fcbc358960210f089a0173f55a0091ea3c0d1 SHA512 ab501640e2db650603899c857866b451fac5c7bbbc7b4ef98559581928869cea49aa326dfca1bb398eee7ebc8843dcc8ee3105c9f462718f1af672aac6b9340a

diff --git a/sci-libs/shogun/files/shogun-4.1.0-remove-C-linkage.patch b/sci-libs/shogun/files/shogun-4.1.0-remove-C-linkage.patch
deleted file mode 100644
index 08edcfac97a..00000000000
--- a/sci-libs/shogun/files/shogun-4.1.0-remove-C-linkage.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Prevent C linkage errors due to templates in extern "C" blocks:
-* /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/bits/cpp_type_traits.h:85:3: error: template with C linkage
-*    template<bool>
-*    ^
-* /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/bits/cpp_type_traits.h:89:3: error: template specialization with C linkage
-*    template<>
-*    ^
-extern "C" blocks can be removed in shogun, as R internally correctly protects C symbols
-
---- shogun-4.1.0/src/interfaces/r_modular/sg_print_functions.cpp
-+++ shogun-4.1.0/src/interfaces/r_modular/sg_print_functions.cpp
-@@ -1,4 +1,3 @@
--extern "C" {
- #include <R.h>
- #include <Rinternals.h>
- #include <Rdefines.h>
-@@ -7,7 +6,6 @@
- #include <Rinterface.h>
- #include <R_ext/RS.h>
- #include <R_ext/Error.h>
--}
- 
- #include <shogun/base/SGObject.h>
- #include <stdio.h>

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
deleted file mode 100644
index 1eb7cd075ec..00000000000
--- a/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-* 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
deleted file mode 100644
index 88454ce87eb..00000000000
--- a/sci-libs/shogun/metadata.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</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-r1.ebuild b/sci-libs/shogun/shogun-5.0.0-r1.ebuild
deleted file mode 100644
index d4e67145a5f..00000000000
--- a/sci-libs/shogun/shogun-5.0.0-r1.ebuild
+++ /dev/null
@@ -1,167 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_6 )
-
-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="https://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"
-RESTRICT="!test? ( 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? (
-		${PYTHON_DEPS}
-		$(python_gen_cond_dep '
-			dev-python/numpy[${PYTHON_MULTI_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? (
-			dev-python/scipy
-		)
-	)
-	R? ( >=dev-lang/swig-3.0.12 )
-	ruby? ( >=dev-lang/swig-3.0.12 )
-	test? (
-		$(python_gen_cond_dep '
-			dev-python/jinja[${PYTHON_MULTI_USEDEP}]
-		')
-		>=dev-cpp/gtest-1.8.0
-	)"
-
-# 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
-}