* [gentoo-commits] repo/gentoo:master commit in: sci-libs/shogun/files/, sci-libs/shogun/
@ 2016-05-07 16:38 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2016-05-07 16:38 UTC (permalink / raw
To: gentoo-commits
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
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-libs/shogun/files/, sci-libs/shogun/
@ 2016-06-05 11:35 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2016-06-05 11:35 UTC (permalink / raw
To: gentoo-commits
commit: efdc6db355ea52656faded3e4408d9a89d527379
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 5 11:29:57 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 5 11:35:06 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=efdc6db3
sci-libs/shogun: Remove extern "C", fix USE="doc" generation
Gentoo-Bug: 582464
Package-Manager: portage-2.3.0_rc1
.../files/shogun-4.1.0-remove-C-linkage.patch | 24 ++++++++++++++++++++++
sci-libs/shogun/shogun-4.1.0.ebuild | 3 ++-
2 files changed, 26 insertions(+), 1 deletion(-)
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
new file mode 100644
index 0000000..08edcfa
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-4.1.0-remove-C-linkage.patch
@@ -0,0 +1,24 @@
+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/shogun-4.1.0.ebuild b/sci-libs/shogun/shogun-4.1.0.ebuild
index 651f7bb..3258b84 100644
--- a/sci-libs/shogun/shogun-4.1.0.ebuild
+++ b/sci-libs/shogun/shogun-4.1.0.ebuild
@@ -78,6 +78,7 @@ DEPEND="${RDEPEND}
PATCHES=(
"${FILESDIR}"/${P}-fix-buildsystem.patch
+ "${FILESDIR}"/${P}-remove-C-linkage.patch
)
pkg_setup() {
@@ -123,5 +124,5 @@ src_configure() {
src_compile() {
cmake-utils_src_compile
- use doc && emake -C doc
+ use doc && emake -C "${BUILD_DIR}"/doc
}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-libs/shogun/files/, sci-libs/shogun/
@ 2017-02-04 21:07 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-02-04 21:07 UTC (permalink / raw
To: gentoo-commits
commit: 9d87880e06967309bde9877094080884b7d9c9ec
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 21:07:13 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9d87880e
sci-libs/shogun: Remove old
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3782
sci-libs/shogun/Manifest | 1 -
sci-libs/shogun/files/shogun-4.1.0-eigen-3.3.patch | 190 ---------------------
.../files/shogun-4.1.0-fix-buildsystem.patch | 81 ---------
sci-libs/shogun/shogun-4.1.0.ebuild | 129 --------------
4 files changed, 401 deletions(-)
diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
index b92de5f..b827f90 100644
--- a/sci-libs/shogun/Manifest
+++ b/sci-libs/shogun/Manifest
@@ -1,3 +1,2 @@
-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-4.1.0-eigen-3.3.patch b/sci-libs/shogun/files/shogun-4.1.0-eigen-3.3.patch
deleted file mode 100644
index ed57cec..00000000
--- a/sci-libs/shogun/files/shogun-4.1.0-eigen-3.3.patch
+++ /dev/null
@@ -1,190 +0,0 @@
-From 57cd0958b153accf12f535ab9406dc8511bf22ec Mon Sep 17 00:00:00 2001
-From: Viktor Gal <viktor.gal@maeth.com>
-Date: Wed, 18 May 2016 06:35:28 +0200
-Subject: [PATCH] Fixing eigen 3.3 related errors
-
-porting fix for #3141 from lisitsyn/tapkee@7c74473d12809e4122527b6e003c74a942d8a25c
-fix #3140: provide a workaround for the eigen bug for calculating log of mapped matrices
----
- src/shogun/lib/tapkee/defines.hpp | 4 +--
- src/shogun/mathematics/eigen3.h | 7 +++++
- .../logdet/opfunc/DenseMatrixExactLog.cpp | 5 ++++
- .../SerialComputationEngine_unittest.cc | 5 ++++
- .../linalg/DenseExactLogJob_unittest.cc | 5 ++++
- .../linalg/RationalApproximation_unittest.cc | 10 ++++++++
- .../linalg/SparseMatrixOperator_unittest.cc | 30 ++++++++++++----------
- 7 files changed, 51 insertions(+), 15 deletions(-)
-
-diff --git a/src/shogun/lib/tapkee/defines.hpp b/src/shogun/lib/tapkee/defines.hpp
-index fd02636..1be45fe 100644
---- a/src/shogun/lib/tapkee/defines.hpp
-+++ b/src/shogun/lib/tapkee/defines.hpp
-@@ -49,12 +49,12 @@ namespace tapkee
- TapkeeOutput(const tapkee::DenseMatrix& e, const tapkee::ProjectingFunction& p) :
- embedding(), projection(p)
- {
-- embedding.swap(e);
-+ embedding = e;
- }
- TapkeeOutput(const TapkeeOutput& that) :
- embedding(), projection(that.projection)
- {
-- this->embedding.swap(that.embedding);
-+ this->embedding = that.embedding;
- }
- tapkee::DenseMatrix embedding;
- tapkee::ProjectingFunction projection;
-diff --git a/src/shogun/mathematics/eigen3.h b/src/shogun/mathematics/eigen3.h
-index 0fb8522..734be6c 100644
---- a/src/shogun/mathematics/eigen3.h
-+++ b/src/shogun/mathematics/eigen3.h
-@@ -61,6 +61,13 @@
-
- #endif //EIGEN_VERSION_AT_LEAST(3,0,93)
-
-+#if ((EIGEN_WORLD_VERSION == 3) && (EIGEN_MAJOR_VERSION == 2) && \
-+ ((EIGEN_MINOR_VERSION == 91) || (EIGEN_MINOR_VERSION == 92)))
-+ // Regression has been introduced to eigen develop (3.3alpha1+):
-+ // http://eigen.tuxfamily.org/bz/show_bug.cgi?id=1229
-+ // until this is not fixed we need to copy the matrix and calculate the log
-+ #define EIGEN_WITH_LOG_BUG_1229 1
-+#endif
- namespace shogun
- {
- template<class T> class SGSparseMatrix;
-diff --git a/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp b/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp
-index a7918e6..1002a6c 100644
---- a/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp
-+++ b/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp
-@@ -62,7 +62,12 @@ void CDenseMatrixExactLog::precompute()
- Map<MatrixXd> mat(m.matrix, m.num_rows, m.num_cols);
- SGMatrix<float64_t> log_m(m.num_rows, m.num_cols);
- Map<MatrixXd> log_mat(log_m.matrix, log_m.num_rows, log_m.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+ MatrixXd tmp = mat;
-+ log_mat=tmp.log();
-+#else
- log_mat=mat.log();
-+#endif
-
- // the log(C) is also a linear operator here
- // reset the operator of this function with log(C)
-diff --git a/tests/unit/lib/computation/SerialComputationEngine_unittest.cc b/tests/unit/lib/computation/SerialComputationEngine_unittest.cc
-index c41a69a..7f96df1 100644
---- a/tests/unit/lib/computation/SerialComputationEngine_unittest.cc
-+++ b/tests/unit/lib/computation/SerialComputationEngine_unittest.cc
-@@ -40,7 +40,12 @@ TEST(SerialComputationEngine, dense_log_det)
- mat(1,1)=3.0;
- Map<MatrixXd> m(mat.matrix, mat.num_rows, mat.num_cols);
- Map<MatrixXd> log_m(log_mat.matrix, log_mat.num_rows, log_mat.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+ MatrixXd tmp = m;
-+ log_m=tmp.log();
-+#else
- log_m=m.log();
-+#endif
-
- // create linear operator and aggregator
- CDenseMatrixOperator<float64_t>* log_op=new CDenseMatrixOperator<float64_t>(log_mat);
-diff --git a/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc b/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc
-index a5a12cf..60daf40 100644
---- a/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc
-+++ b/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc
-@@ -38,7 +38,12 @@ TEST(DenseExactLogJob, log_det)
- mat(1,1)=3.0;
- Map<MatrixXd> m(mat.matrix, mat.num_rows, mat.num_cols);
- Map<MatrixXd> log_m(log_mat.matrix, log_mat.num_rows, log_mat.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+ MatrixXd tmp = m;
-+ log_m=tmp.log();
-+#else
- log_m=m.log();
-+#endif
-
- // create linear operator and aggregator
- CDenseMatrixOperator<float64_t>* log_op=new CDenseMatrixOperator<float64_t>(log_mat);
-diff --git a/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc b/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc
-index f401d06..682ed66 100644
---- a/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc
-+++ b/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc
-@@ -182,7 +182,12 @@ TEST(RationalApproximation, trace_accuracy)
- #if EIGEN_VERSION_AT_LEAST(3,1,0)
- // compute the trace of log(m) using Eigen3 that uses Schur-Parlett algorithm
- Map<MatrixXd> eig_m(m.matrix, m.num_rows, m.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+ MatrixXd tmp = eig_m;
-+ float64_t trace_log_m=tmp.log().diagonal().sum();
-+#else
- float64_t trace_log_m=eig_m.log().diagonal().sum();
-+#endif
- #else
- float64_t trace_log_m=-11.51292546497021618279;
- #endif // EIGEN_VERSION_AT_LEAST(3,1,0)
-@@ -364,7 +369,12 @@ TEST(RationalApproximation, trace_accuracy_cg_m)
- #if EIGEN_VERSION_AT_LEAST(3,1,0)
- // compute the trace of log(m) using Eigen3 that uses Schur-Parlett algorithm
- Map<MatrixXd> eig_m(m.matrix, m.num_rows, m.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+ MatrixXd tmp = eig_m;
-+ float64_t trace_log_m=tmp.log().diagonal().sum();
-+#else
- float64_t trace_log_m=eig_m.log().diagonal().sum();
-+#endif
- #else
- float64_t trace_log_m=-11.51292546497021618279;
- #endif // EIGEN_VERSION_AT_LEAST(3,1,0)
-diff --git a/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc b/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc
-index 4d30724..9d171cc 100644
---- a/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc
-+++ b/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc
-@@ -219,33 +219,37 @@ TEST(SparseMatrixOperator, get_set_diagonal_realloc_complex128)
-
- TEST(SparseMatrixOperator, get_sparsity_structure)
- {
-- const int size=9;
-- const int max_pow=10;
-+ const int32_t size=9;
-+ const int32_t max_pow=10;
-
-- SGMatrix<double> m(size, size);
-+ SGMatrix<float64_t> m(size, size);
-
- m.set_const(0.0);
-- for (int i=0; i<size; ++i)
-+ for (int32_t i=0; i<size; ++i)
- m(i,i)=2.0;
-- for (int i=0; i<size; i+=4)
-+ for (int32_t i=0; i<size; i+=4)
- m(i,size-1)=2.0;
-- for (int i=0; i<size; i+=4)
-+ for (int32_t i=0; i<size; i+=4)
- m(size-1,i)=2.0;
-
-- CSparseFeatures<double> feat(m);
-- SGSparseMatrix<double> sm=feat.get_sparse_feature_matrix();
-- CSparseMatrixOperator<double> op(sm);
-+ CSparseFeatures<float64_t> feat(m);
-+ SGSparseMatrix<float64_t> sm=feat.get_sparse_feature_matrix();
-+ CSparseMatrixOperator<float64_t> op(sm);
- CSparseMatrixOperator<bool>* b_op
- =static_cast<CSparseMatrixOperator<bool>*>(op);
-
-- SparseMatrix<bool, RowMajor, int> sp
-+ SparseMatrix<bool, RowMajor, int32_t> sp
- =EigenSparseUtil<bool>::toEigenSparse(b_op->get_matrix_operator());
-- SparseMatrix<double, RowMajor, int> sm2
-- =EigenSparseUtil<double>::toEigenSparse(sm);
-+ SparseMatrix<float64_t, RowMajor, int32_t> sm2
-+ =EigenSparseUtil<float64_t>::toEigenSparse(sm);
-
- // compute direct matrix power and then the sparsity structure
-- for (int i=2; i<=max_pow; ++i)
-+ for (int32_t i=2; i<=max_pow; ++i)
-+#if EIGEN_VERSION_AT_LEAST(3,2,91)
-+ sp=(sp.cast<float64_t>()*sm2).cast<bool>();
-+#else
- sp=sp*sm2;
-+#endif
-
- int32_t* outerIndexPtr=const_cast<int32_t*>(sp.outerIndexPtr());
- int32_t* innerIndexPtr=const_cast<int32_t*>(sp.innerIndexPtr());
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
deleted file mode 100644
index e244c94..00000000
--- a/sci-libs/shogun/files/shogun-4.1.0-fix-buildsystem.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-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
deleted file mode 100644
index 3f31f9d..00000000
--- a/sci-libs/shogun/shogun-4.1.0.ebuild
+++ /dev/null
@@ -1,129 +0,0 @@
-# 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="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
- "${FILESDIR}"/${P}-remove-C-linkage.patch
- "${FILESDIR}"/${P}-eigen-3.3.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 "${BUILD_DIR}"/doc
-}
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