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 <[email protected]> (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 <[email protected]> (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>[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-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 -}
