Gentoo Archives: gentoo-commits

From: "Michał Górny" <mgorny@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-libs/shogun/, sci-libs/shogun/files/, profiles/
Date: Sun, 25 Oct 2020 14:50:36
Message-Id: 1603637426.524551cf255750e37c074627fe801b0d21512228.mgorny@gentoo
1 commit: 524551cf255750e37c074627fe801b0d21512228
2 Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
3 AuthorDate: Sun Oct 25 14:49:59 2020 +0000
4 Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
5 CommitDate: Sun Oct 25 14:50:26 2020 +0000
6 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=524551cf
7
8 sci-libs/shogun: Remove last-rited pkg
9
10 Closes: https://bugs.gentoo.org/737412
11 Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
12
13 profiles/package.mask | 6 -
14 sci-libs/shogun/Manifest | 2 -
15 .../files/shogun-4.1.0-remove-C-linkage.patch | 24 ---
16 .../files/shogun-5.0.0-fix-buildsystem.patch | 72 ---------
17 sci-libs/shogun/metadata.xml | 32 ----
18 sci-libs/shogun/shogun-5.0.0-r1.ebuild | 167 ---------------------
19 6 files changed, 303 deletions(-)
20
21 diff --git a/profiles/package.mask b/profiles/package.mask
22 index e5dc1cdd1a7..6599f3e8381 100644
23 --- a/profiles/package.mask
24 +++ b/profiles/package.mask
25 @@ -252,12 +252,6 @@ sys-apps/lcdtest
26 =dev-python/pypy3-exe-7.3.2_p37*
27 =dev-python/pypy3-exe-bin-7.3.2_p37*
28
29 -# Michał Górny <mgorny@g.o> (2020-09-25)
30 -# Effectively unmaintained. Not ported to py3.7. Multiple unresolved
31 -# build failures reported. No reverse dependencies.
32 -# Removal in 30 days. Bug #737412.
33 -sci-libs/shogun
34 -
35 # Michał Górny <mgorny@g.o> (2020-09-09)
36 # These packages (or package versions) still require Python 2.7.
37 # They are either dead upstream, their Python 3 porting efforts are
38
39 diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
40 deleted file mode 100644
41 index 8a9281c8d29..00000000000
42 --- a/sci-libs/shogun/Manifest
43 +++ /dev/null
44 @@ -1,2 +0,0 @@
45 -DIST shogun-5.0.0.tar.bz2 2448509 BLAKE2B 85352d782740b4c671bb6081e0445bb7e801e27e36fdc0f82658b937fd6658c41016e4a91841ddb09ae9062b77d32f290f56b191318c1c34bf0812d1b9a8b364 SHA512 fa8d9dee4596acce12022540a6927cbdb62e08f8468c8be3790de07ebf3a53055032bcc532b28334ca83284c38f2b0153602634f12bafe4019acb9121b9ff236
46 -DIST shogun-data-0.9.tar.bz2 287533841 BLAKE2B 796830262205961b88715f4eb60a47ff2ad108426b7af8e4e1a0733920962ad8154a1ab9892356e9793be24d415fcbc358960210f089a0173f55a0091ea3c0d1 SHA512 ab501640e2db650603899c857866b451fac5c7bbbc7b4ef98559581928869cea49aa326dfca1bb398eee7ebc8843dcc8ee3105c9f462718f1af672aac6b9340a
47
48 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
49 deleted file mode 100644
50 index 08edcfac97a..00000000000
51 --- a/sci-libs/shogun/files/shogun-4.1.0-remove-C-linkage.patch
52 +++ /dev/null
53 @@ -1,24 +0,0 @@
54 -Prevent C linkage errors due to templates in extern "C" blocks:
55 -* /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
56 -* template<bool>
57 -* ^
58 -* /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
59 -* template<>
60 -* ^
61 -extern "C" blocks can be removed in shogun, as R internally correctly protects C symbols
62 -
63 ---- shogun-4.1.0/src/interfaces/r_modular/sg_print_functions.cpp
64 -+++ shogun-4.1.0/src/interfaces/r_modular/sg_print_functions.cpp
65 -@@ -1,4 +1,3 @@
66 --extern "C" {
67 - #include <R.h>
68 - #include <Rinternals.h>
69 - #include <Rdefines.h>
70 -@@ -7,7 +6,6 @@
71 - #include <Rinterface.h>
72 - #include <R_ext/RS.h>
73 - #include <R_ext/Error.h>
74 --}
75 -
76 - #include <shogun/base/SGObject.h>
77 - #include <stdio.h>
78
79 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
80 deleted file mode 100644
81 index 1eb7cd075ec..00000000000
82 --- a/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch
83 +++ /dev/null
84 @@ -1,72 +0,0 @@
85 -* Remove setting of user flags
86 -* Remove erroneous bundling of Eigen
87 -
88 ---- a/CMakeLists.txt
89 -+++ b/CMakeLists.txt
90 -@@ -33,15 +33,6 @@
91 - SET(EIGEN_VERSION_MINIMUM 3.1.2)
92 - SET(VIENNACL_VERSION_MINIMUM 1.5.0)
93 -
94 --# Store system's or distribution's C[XX]FLAGS.
95 --SET(SYSTEM_C_FLAGS "${CMAKE_C_FLAGS}")
96 --SET(SYSTEM_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
97 --STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE_UC)
98 --IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
99 -- SET(CMAKE_C_FLAGS "")
100 -- SET(CMAKE_CXX_FLAGS "")
101 --ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
102 --
103 - # CCACHE
104 - OPTION(ENABLE_CCACHE "Enable ccache for compilation" ON)
105 - FIND_PACKAGE(CCache)
106 -@@ -174,24 +165,6 @@
107 - SET(COMPILER_WARNINGS "-Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated")
108 - ENDIF()
109 -
110 --IF(CMAKE_COMPILER_IS_GNUCXX)
111 -- SET(RELEASE_COMPILER_FLAGS "-fexpensive-optimizations -frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2 -fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops")
112 -- IF (${MACHINE} MATCHES "x86_64" OR ${MACHINE} MATCHES "i686")
113 -- SET(RELEASE_COMPILER_FLAGS "${RELEASE_COMPILER_FLAGS} -mfpmath=sse")
114 -- ENDIF()
115 --ELSEIF(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
116 -- SET(RELEASE_COMPILER_FLAGS "-funroll-loops")
117 --ENDIF()
118 --SET(SWIG_CXX_COMPILER_FLAGS "-O0 -g")
119 --SET(CMAKE_C_FLAGS "${COMPILER_WARNINGS} ${CMAKE_C_FLAGS}")
120 --SET(CMAKE_CXX_FLAGS "${COMPILER_WARNINGS} ${CMAKE_CXX_FLAGS}")
121 --SET(CMAKE_C_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
122 --SET(CMAKE_CXX_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
123 --SET(CMAKE_C_FLAGS_DISTRIBUTION "-O2")
124 --SET(CMAKE_CXX_FLAGS_DISTRIBUTION "-O2")
125 --SET(CMAKE_C_FLAGS_DEBUG "-g")
126 --SET(CMAKE_CXX_FLAGS_DEBUG "-g")
127 --
128 - OPTION(ENABLE_COVERAGE "Enable code coverage" OFF)
129 - IF(ENABLE_COVERAGE)
130 - IF(NOT CMAKE_COMPILER_IS_GNUCXX)
131 -@@ -617,13 +590,6 @@
132 - include(external/Eigen3)
133 - LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR})
134 - ELSE()
135 -- # eigen3 bug related to aliasing operators and self-storing.
136 -- # TODO put in proper reference and version from when this is fixed
137 -- IF(${EIGEN_VERSION} VERSION_GREATER 3.2.90)
138 -- MESSAGE(WARNING "The system Eigen3 version ${EIGEN_VERSION} is buggy, manually bundling.")
139 -- include(external/Eigen3)
140 -- ENDIF()
141 --
142 - LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR})
143 - ENDIF()
144 -
145 -@@ -957,11 +923,6 @@
146 - # Respect system's or distribution's C[XX]FLAGS.
147 - OPTION(SWIG_WITH_SYSTEM_CFLAGS "Enable system's C[XX]FLAGS for compilation of swig-binaries" ON)
148 -
149 --IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
150 -- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${SYSTEM_C_FLAGS}")
151 -- SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SYSTEM_CXX_FLAGS}")
152 --ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
153 --
154 - IF(SWIG_WITH_SYSTEM_CFLAGS)
155 - SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS} ${SYSTEM_CXX_FLAGS}")
156 - ENDIF(SWIG_WITH_SYSTEM_CFLAGS)
157
158 diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml
159 deleted file mode 100644
160 index 88454ce87eb..00000000000
161 --- a/sci-libs/shogun/metadata.xml
162 +++ /dev/null
163 @@ -1,32 +0,0 @@
164 -<?xml version="1.0" encoding="UTF-8"?>
165 -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
166 -<pkgmetadata>
167 - <maintainer type="project">
168 - <email>sci@g.o</email>
169 - <name>Gentoo Science Project</name>
170 - </maintainer>
171 - <longdescription lang="en">
172 - SHOGUN - is a new machine learning toolbox with focus on large
173 - scale kernel methods and especially on Support Vector Machines
174 - (SVM) with focus to bioinformatics. It provides a generic SVM
175 - object interfacing to several different SVM implementations. Each
176 - of the SVMs can be combined with a variety of the many kernels
177 - implemented. It can deal with weighted linear combination of a
178 - number of sub-kernels, each of which not necessarily working on the
179 - same domain, where an optimal sub-kernel weighting can be learned
180 - using Multiple Kernel Learning. Apart from SVM 2-class
181 - classification and regression problems, a number of linear methods
182 - like Linear Discriminant Analysis (LDA), Linear Programming Machine
183 - (LPM), (Kernel) Perceptrons and also algorithms to train hidden
184 - markov models are implemented. The input feature-objects can be
185 - dense, sparse or strings and of type int/short/double/char and can
186 - be converted into different feature types. Chains of preprocessors
187 - (e.g. substracting the mean) can be attached to each feature object
188 - allowing for on-the-fly pre-processing.
189 - </longdescription>
190 - <use>
191 - <flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag>
192 - <flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag>
193 - <flag name="opencl">Enable support for building against OpenCL</flag>
194 - </use>
195 -</pkgmetadata>
196
197 diff --git a/sci-libs/shogun/shogun-5.0.0-r1.ebuild b/sci-libs/shogun/shogun-5.0.0-r1.ebuild
198 deleted file mode 100644
199 index d4e67145a5f..00000000000
200 --- a/sci-libs/shogun/shogun-5.0.0-r1.ebuild
201 +++ /dev/null
202 @@ -1,167 +0,0 @@
203 -# Copyright 1999-2020 Gentoo Authors
204 -# Distributed under the terms of the GNU General Public License v2
205 -
206 -EAPI=6
207 -
208 -PYTHON_COMPAT=( python3_6 )
209 -
210 -inherit cmake-utils flag-o-matic python-single-r1 toolchain-funcs versionator
211 -
212 -MYPV=$(get_version_component_range 1-2)
213 -MYPD=${PN}-data-0.9
214 -
215 -DESCRIPTION="Large Scale Machine Learning Toolbox"
216 -HOMEPAGE="https://shogun-toolbox.org/"
217 -SRC_URI="
218 - ftp://shogun-toolbox.org/shogun/releases/${MYPV}/sources/${P}.tar.bz2
219 - test? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )
220 - examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )"
221 -
222 -LICENSE="GPL-3 free-noncomm"
223 -SLOT="0/16"
224 -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
225 -IUSE="cpu_flags_x86_sse doc examples lua octave opencl python R ruby static-libs test"
226 -RESTRICT="!test? ( test )"
227 -
228 -REQUIRED_USE="
229 - python? ( ${PYTHON_REQUIRED_USE} )
230 - test? ( python )"
231 -
232 -RDEPEND="
233 - app-arch/bzip2
234 - app-arch/gzip
235 - app-arch/lzma
236 - app-arch/snappy
237 - dev-libs/lzo
238 - dev-cpp/eigen:3
239 - dev-libs/json-c:=
240 - dev-libs/libxml2
241 - dev-libs/protobuf:=
242 - net-misc/curl
243 - sci-libs/arpack
244 - sci-libs/arprec
245 - sci-libs/colpack
246 - sci-libs/hdf5:=
247 - sci-libs/nlopt
248 - sci-mathematics/glpk:=
249 - sci-mathematics/lpsolve:=
250 - sys-libs/readline:0=
251 - sys-libs/zlib
252 - virtual/blas
253 - virtual/cblas
254 - virtual/lapack
255 - lua? ( dev-lang/lua:0 )
256 - octave? ( >=sci-mathematics/octave-4.2.0:=[hdf5] )
257 - opencl? ( virtual/opencl )
258 - python? (
259 - ${PYTHON_DEPS}
260 - $(python_gen_cond_dep '
261 - dev-python/numpy[${PYTHON_MULTI_USEDEP}]
262 - ')
263 - )
264 - R? ( dev-lang/R )
265 - ruby? ( dev-ruby/narray )"
266 -DEPEND="${RDEPEND}
267 - virtual/pkgconfig
268 - doc? (
269 - >=app-doc/doxygen-1.8.13-r1[dot]
270 - dev-python/sphinx
271 - )
272 - lua? ( >=dev-lang/swig-3.0.12 )
273 - octave? ( >=dev-lang/swig-3.0.12 )
274 - python? (
275 - >=dev-lang/swig-3.0.12
276 - test? (
277 - dev-python/scipy
278 - )
279 - )
280 - R? ( >=dev-lang/swig-3.0.12 )
281 - ruby? ( >=dev-lang/swig-3.0.12 )
282 - test? (
283 - $(python_gen_cond_dep '
284 - dev-python/jinja[${PYTHON_MULTI_USEDEP}]
285 - ')
286 - >=dev-cpp/gtest-1.8.0
287 - )"
288 -
289 -# javamodular needs jblas (painful to package properly)
290 -# permodular work in progress (as 3.2.0)
291 -# could actually support multiple pythons, multiple rubys
292 -# feel free to do work for it
293 -
294 -PATCHES=(
295 - "${FILESDIR}"/${PN}-5.0.0-fix-buildsystem.patch
296 - "${FILESDIR}"/${PN}-4.1.0-remove-C-linkage.patch
297 -)
298 -
299 -pkg_setup() {
300 - use python && python-single-r1_pkg_setup
301 -}
302 -
303 -src_configure() {
304 - export ATLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas lapack)"
305 - export CBLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas)"
306 - export ATLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas cblas lapack)"
307 - export LAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
308 -
309 - append-cppflags "$($(tc-getPKG_CONFIG) --cflags cblas)"
310 -
311 - local mycmakeargs=(
312 - -DCMAKE_SKIP_RPATH=ON
313 - -DCMAKE_SKIP_INSTALL_RPATH=ON
314 - -DLIB_INSTALL_DIR=$(get_libdir)
315 - -DENABLE_TESTING=$(usex test)
316 - -DBUILD_EXAMPLES=$(usex examples)
317 - -DDISABLE_SSE=$(usex !cpu_flags_x86_sse)
318 - -DCMAKE_DISABLE_FIND_PACKAGE_Pandoc=ON
319 - $(cmake-utils_use_find_package doc Sphinx)
320 - $(cmake-utils_use_find_package doc Doxygen)
321 -
322 - # Features:
323 - -DENABLE_COVERAGE=OFF
324 - -DENABLE_COLPACK=ON
325 - -DENABLE_PROTOBUF=ON
326 - -DENABLE_PYTHON_DEBUG=OFF
327 - -DENABLE_VIENNACL=$(usex opencl)
328 - -DUSE_ARPREC=ON
329 - -DUSE_HDF5=ON
330 -
331 - # Bindings:
332 - -DJavaModular=OFF
333 - -DPerlModular=OFF
334 - -DCSharpModular=OFF
335 - -DLuaModular=$(usex lua)
336 - -DOctaveModular=$(usex octave)
337 - -DPythonModular=$(usex python)
338 - -DRModular=$(usex R)
339 - -DRubyModular=$(usex ruby)
340 -
341 - # Disable bundled libs
342 - -DBUNDLE_COLPACK=OFF
343 - -DBUNDLE_JSON=OFF
344 - -DBUNDLE_NLOPT=OFF
345 - )
346 - cmake-utils_src_configure
347 -
348 - # gentoo bug #302621
349 - has_version 'sci-libs/hdf5[mpi]' && export CXX=mpicxx CC=mpicc
350 -}
351 -
352 -src_compile() {
353 - cmake-utils_src_compile
354 - use doc && cmake-utils_src_compile -C doc
355 -}
356 -
357 -src_install() {
358 - cmake-utils_src_install
359 -
360 - if use doc; then
361 - local i
362 - for i in lua octave python R ruby; do
363 - if use $i; then
364 - docinto html/${i,}_modular
365 - dodoc -r "${BUILD_DIR}"/src/interfaces/${i,}_modular/modshogun/doxygen_xml/.
366 - fi
367 - done
368 - fi
369 -}