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commit: 524551cf255750e37c074627fe801b0d21512228 |
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Author: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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AuthorDate: Sun Oct 25 14:49:59 2020 +0000 |
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Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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CommitDate: Sun Oct 25 14:50:26 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=524551cf |
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|
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sci-libs/shogun: Remove last-rited pkg |
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|
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Closes: https://bugs.gentoo.org/737412 |
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Signed-off-by: Michał Górny <mgorny <AT> gentoo.org> |
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|
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profiles/package.mask | 6 - |
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sci-libs/shogun/Manifest | 2 - |
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.../files/shogun-4.1.0-remove-C-linkage.patch | 24 --- |
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.../files/shogun-5.0.0-fix-buildsystem.patch | 72 --------- |
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sci-libs/shogun/metadata.xml | 32 ---- |
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sci-libs/shogun/shogun-5.0.0-r1.ebuild | 167 --------------------- |
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6 files changed, 303 deletions(-) |
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|
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diff --git a/profiles/package.mask b/profiles/package.mask |
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index e5dc1cdd1a7..6599f3e8381 100644 |
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--- a/profiles/package.mask |
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+++ b/profiles/package.mask |
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@@ -252,12 +252,6 @@ sys-apps/lcdtest |
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=dev-python/pypy3-exe-7.3.2_p37* |
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=dev-python/pypy3-exe-bin-7.3.2_p37* |
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|
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-# Michał Górny <mgorny@g.o> (2020-09-25) |
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-# Effectively unmaintained. Not ported to py3.7. Multiple unresolved |
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-# build failures reported. No reverse dependencies. |
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-# Removal in 30 days. Bug #737412. |
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-sci-libs/shogun |
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- |
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# Michał Górny <mgorny@g.o> (2020-09-09) |
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# These packages (or package versions) still require Python 2.7. |
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# They are either dead upstream, their Python 3 porting efforts are |
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|
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diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest |
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deleted file mode 100644 |
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index 8a9281c8d29..00000000000 |
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--- a/sci-libs/shogun/Manifest |
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+++ /dev/null |
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@@ -1,2 +0,0 @@ |
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-DIST shogun-5.0.0.tar.bz2 2448509 BLAKE2B 85352d782740b4c671bb6081e0445bb7e801e27e36fdc0f82658b937fd6658c41016e4a91841ddb09ae9062b77d32f290f56b191318c1c34bf0812d1b9a8b364 SHA512 fa8d9dee4596acce12022540a6927cbdb62e08f8468c8be3790de07ebf3a53055032bcc532b28334ca83284c38f2b0153602634f12bafe4019acb9121b9ff236 |
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-DIST shogun-data-0.9.tar.bz2 287533841 BLAKE2B 796830262205961b88715f4eb60a47ff2ad108426b7af8e4e1a0733920962ad8154a1ab9892356e9793be24d415fcbc358960210f089a0173f55a0091ea3c0d1 SHA512 ab501640e2db650603899c857866b451fac5c7bbbc7b4ef98559581928869cea49aa326dfca1bb398eee7ebc8843dcc8ee3105c9f462718f1af672aac6b9340a |
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|
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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 |
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deleted file mode 100644 |
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index 08edcfac97a..00000000000 |
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--- a/sci-libs/shogun/files/shogun-4.1.0-remove-C-linkage.patch |
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+++ /dev/null |
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@@ -1,24 +0,0 @@ |
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-Prevent C linkage errors due to templates in extern "C" blocks: |
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-* /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 |
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-* template<bool> |
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-* ^ |
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-* /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 |
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-* template<> |
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-* ^ |
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-extern "C" blocks can be removed in shogun, as R internally correctly protects C symbols |
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- |
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---- shogun-4.1.0/src/interfaces/r_modular/sg_print_functions.cpp |
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-+++ shogun-4.1.0/src/interfaces/r_modular/sg_print_functions.cpp |
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-@@ -1,4 +1,3 @@ |
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--extern "C" { |
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- #include <R.h> |
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- #include <Rinternals.h> |
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- #include <Rdefines.h> |
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-@@ -7,7 +6,6 @@ |
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- #include <Rinterface.h> |
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- #include <R_ext/RS.h> |
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- #include <R_ext/Error.h> |
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--} |
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- |
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- #include <shogun/base/SGObject.h> |
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- #include <stdio.h> |
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|
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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 |
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deleted file mode 100644 |
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index 1eb7cd075ec..00000000000 |
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--- a/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch |
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+++ /dev/null |
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@@ -1,72 +0,0 @@ |
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-* Remove setting of user flags |
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-* Remove erroneous bundling of Eigen |
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- |
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---- a/CMakeLists.txt |
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-+++ b/CMakeLists.txt |
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-@@ -33,15 +33,6 @@ |
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- SET(EIGEN_VERSION_MINIMUM 3.1.2) |
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- SET(VIENNACL_VERSION_MINIMUM 1.5.0) |
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- |
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--# Store system's or distribution's C[XX]FLAGS. |
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--SET(SYSTEM_C_FLAGS "${CMAKE_C_FLAGS}") |
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--SET(SYSTEM_CXX_FLAGS "${CMAKE_CXX_FLAGS}") |
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--STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE_UC) |
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--IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION")) |
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-- SET(CMAKE_C_FLAGS "") |
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-- SET(CMAKE_CXX_FLAGS "") |
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--ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION")) |
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-- |
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- # CCACHE |
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- OPTION(ENABLE_CCACHE "Enable ccache for compilation" ON) |
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- FIND_PACKAGE(CCache) |
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-@@ -174,24 +165,6 @@ |
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- SET(COMPILER_WARNINGS "-Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated") |
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- ENDIF() |
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- |
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--IF(CMAKE_COMPILER_IS_GNUCXX) |
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-- SET(RELEASE_COMPILER_FLAGS "-fexpensive-optimizations -frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2 -fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops") |
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-- IF (${MACHINE} MATCHES "x86_64" OR ${MACHINE} MATCHES "i686") |
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-- SET(RELEASE_COMPILER_FLAGS "${RELEASE_COMPILER_FLAGS} -mfpmath=sse") |
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-- ENDIF() |
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--ELSEIF(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang") |
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-- SET(RELEASE_COMPILER_FLAGS "-funroll-loops") |
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--ENDIF() |
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--SET(SWIG_CXX_COMPILER_FLAGS "-O0 -g") |
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--SET(CMAKE_C_FLAGS "${COMPILER_WARNINGS} ${CMAKE_C_FLAGS}") |
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--SET(CMAKE_CXX_FLAGS "${COMPILER_WARNINGS} ${CMAKE_CXX_FLAGS}") |
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--SET(CMAKE_C_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}") |
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--SET(CMAKE_CXX_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}") |
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--SET(CMAKE_C_FLAGS_DISTRIBUTION "-O2") |
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--SET(CMAKE_CXX_FLAGS_DISTRIBUTION "-O2") |
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--SET(CMAKE_C_FLAGS_DEBUG "-g") |
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--SET(CMAKE_CXX_FLAGS_DEBUG "-g") |
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-- |
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- OPTION(ENABLE_COVERAGE "Enable code coverage" OFF) |
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- IF(ENABLE_COVERAGE) |
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- IF(NOT CMAKE_COMPILER_IS_GNUCXX) |
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-@@ -617,13 +590,6 @@ |
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- include(external/Eigen3) |
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- LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR}) |
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- ELSE() |
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-- # eigen3 bug related to aliasing operators and self-storing. |
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-- # TODO put in proper reference and version from when this is fixed |
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-- IF(${EIGEN_VERSION} VERSION_GREATER 3.2.90) |
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-- MESSAGE(WARNING "The system Eigen3 version ${EIGEN_VERSION} is buggy, manually bundling.") |
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-- include(external/Eigen3) |
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-- ENDIF() |
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-- |
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- LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR}) |
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- ENDIF() |
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- |
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-@@ -957,11 +923,6 @@ |
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- # Respect system's or distribution's C[XX]FLAGS. |
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- OPTION(SWIG_WITH_SYSTEM_CFLAGS "Enable system's C[XX]FLAGS for compilation of swig-binaries" ON) |
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- |
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--IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION")) |
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-- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${SYSTEM_C_FLAGS}") |
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-- SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SYSTEM_CXX_FLAGS}") |
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--ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION")) |
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-- |
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- IF(SWIG_WITH_SYSTEM_CFLAGS) |
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- SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS} ${SYSTEM_CXX_FLAGS}") |
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- ENDIF(SWIG_WITH_SYSTEM_CFLAGS) |
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|
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diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml |
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deleted file mode 100644 |
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index 88454ce87eb..00000000000 |
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--- a/sci-libs/shogun/metadata.xml |
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+++ /dev/null |
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@@ -1,32 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <maintainer type="project"> |
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- <email>sci@g.o</email> |
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- <name>Gentoo Science Project</name> |
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- </maintainer> |
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- <longdescription lang="en"> |
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- SHOGUN - is a new machine learning toolbox with focus on large |
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- scale kernel methods and especially on Support Vector Machines |
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- (SVM) with focus to bioinformatics. It provides a generic SVM |
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- object interfacing to several different SVM implementations. Each |
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- of the SVMs can be combined with a variety of the many kernels |
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- implemented. It can deal with weighted linear combination of a |
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- number of sub-kernels, each of which not necessarily working on the |
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- same domain, where an optimal sub-kernel weighting can be learned |
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- using Multiple Kernel Learning. Apart from SVM 2-class |
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- classification and regression problems, a number of linear methods |
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- like Linear Discriminant Analysis (LDA), Linear Programming Machine |
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- (LPM), (Kernel) Perceptrons and also algorithms to train hidden |
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- markov models are implemented. The input feature-objects can be |
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- dense, sparse or strings and of type int/short/double/char and can |
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- be converted into different feature types. Chains of preprocessors |
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- (e.g. substracting the mean) can be attached to each feature object |
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- allowing for on-the-fly pre-processing. |
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- </longdescription> |
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- <use> |
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- <flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag> |
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- <flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag> |
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- <flag name="opencl">Enable support for building against OpenCL</flag> |
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- </use> |
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-</pkgmetadata> |
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|
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diff --git a/sci-libs/shogun/shogun-5.0.0-r1.ebuild b/sci-libs/shogun/shogun-5.0.0-r1.ebuild |
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deleted file mode 100644 |
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index d4e67145a5f..00000000000 |
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--- a/sci-libs/shogun/shogun-5.0.0-r1.ebuild |
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+++ /dev/null |
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@@ -1,167 +0,0 @@ |
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-# Copyright 1999-2020 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=6 |
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- |
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-PYTHON_COMPAT=( python3_6 ) |
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- |
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-inherit cmake-utils flag-o-matic python-single-r1 toolchain-funcs versionator |
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- |
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-MYPV=$(get_version_component_range 1-2) |
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-MYPD=${PN}-data-0.9 |
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- |
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-DESCRIPTION="Large Scale Machine Learning Toolbox" |
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-HOMEPAGE="https://shogun-toolbox.org/" |
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-SRC_URI=" |
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- ftp://shogun-toolbox.org/shogun/releases/${MYPV}/sources/${P}.tar.bz2 |
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- test? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 ) |
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- examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )" |
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- |
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-LICENSE="GPL-3 free-noncomm" |
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-SLOT="0/16" |
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-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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-IUSE="cpu_flags_x86_sse doc examples lua octave opencl python R ruby static-libs test" |
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-RESTRICT="!test? ( test )" |
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- |
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-REQUIRED_USE=" |
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- python? ( ${PYTHON_REQUIRED_USE} ) |
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- test? ( python )" |
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- |
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-RDEPEND=" |
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- app-arch/bzip2 |
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- app-arch/gzip |
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- app-arch/lzma |
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- app-arch/snappy |
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- dev-libs/lzo |
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- dev-cpp/eigen:3 |
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- dev-libs/json-c:= |
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- dev-libs/libxml2 |
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- dev-libs/protobuf:= |
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- net-misc/curl |
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- sci-libs/arpack |
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- sci-libs/arprec |
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- sci-libs/colpack |
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- sci-libs/hdf5:= |
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- sci-libs/nlopt |
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- sci-mathematics/glpk:= |
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- sci-mathematics/lpsolve:= |
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- sys-libs/readline:0= |
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- sys-libs/zlib |
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- virtual/blas |
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- virtual/cblas |
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- virtual/lapack |
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- lua? ( dev-lang/lua:0 ) |
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- octave? ( >=sci-mathematics/octave-4.2.0:=[hdf5] ) |
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- opencl? ( virtual/opencl ) |
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- python? ( |
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- ${PYTHON_DEPS} |
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- $(python_gen_cond_dep ' |
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- dev-python/numpy[${PYTHON_MULTI_USEDEP}] |
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- ') |
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- ) |
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- R? ( dev-lang/R ) |
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- ruby? ( dev-ruby/narray )" |
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-DEPEND="${RDEPEND} |
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- virtual/pkgconfig |
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- doc? ( |
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- >=app-doc/doxygen-1.8.13-r1[dot] |
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- dev-python/sphinx |
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- ) |
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- lua? ( >=dev-lang/swig-3.0.12 ) |
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- octave? ( >=dev-lang/swig-3.0.12 ) |
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- python? ( |
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- >=dev-lang/swig-3.0.12 |
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- test? ( |
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- dev-python/scipy |
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- ) |
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- ) |
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- R? ( >=dev-lang/swig-3.0.12 ) |
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- ruby? ( >=dev-lang/swig-3.0.12 ) |
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- test? ( |
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- $(python_gen_cond_dep ' |
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- dev-python/jinja[${PYTHON_MULTI_USEDEP}] |
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- ') |
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- >=dev-cpp/gtest-1.8.0 |
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- )" |
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- |
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-# javamodular needs jblas (painful to package properly) |
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-# permodular work in progress (as 3.2.0) |
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-# could actually support multiple pythons, multiple rubys |
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-# feel free to do work for it |
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- |
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-PATCHES=( |
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- "${FILESDIR}"/${PN}-5.0.0-fix-buildsystem.patch |
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- "${FILESDIR}"/${PN}-4.1.0-remove-C-linkage.patch |
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-) |
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- |
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-pkg_setup() { |
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- use python && python-single-r1_pkg_setup |
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-} |
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- |
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-src_configure() { |
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- export ATLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas lapack)" |
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- export CBLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas)" |
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- export ATLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas cblas lapack)" |
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- export LAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" |
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- |
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- append-cppflags "$($(tc-getPKG_CONFIG) --cflags cblas)" |
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- |
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- local mycmakeargs=( |
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- -DCMAKE_SKIP_RPATH=ON |
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- -DCMAKE_SKIP_INSTALL_RPATH=ON |
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- -DLIB_INSTALL_DIR=$(get_libdir) |
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- -DENABLE_TESTING=$(usex test) |
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- -DBUILD_EXAMPLES=$(usex examples) |
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- -DDISABLE_SSE=$(usex !cpu_flags_x86_sse) |
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- -DCMAKE_DISABLE_FIND_PACKAGE_Pandoc=ON |
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- $(cmake-utils_use_find_package doc Sphinx) |
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- $(cmake-utils_use_find_package doc Doxygen) |
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- |
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- # Features: |
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- -DENABLE_COVERAGE=OFF |
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- -DENABLE_COLPACK=ON |
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- -DENABLE_PROTOBUF=ON |
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- -DENABLE_PYTHON_DEBUG=OFF |
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- -DENABLE_VIENNACL=$(usex opencl) |
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- -DUSE_ARPREC=ON |
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- -DUSE_HDF5=ON |
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- |
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- # Bindings: |
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- -DJavaModular=OFF |
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- -DPerlModular=OFF |
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- -DCSharpModular=OFF |
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- -DLuaModular=$(usex lua) |
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- -DOctaveModular=$(usex octave) |
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- -DPythonModular=$(usex python) |
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- -DRModular=$(usex R) |
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- -DRubyModular=$(usex ruby) |
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- |
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- # Disable bundled libs |
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- -DBUNDLE_COLPACK=OFF |
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- -DBUNDLE_JSON=OFF |
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- -DBUNDLE_NLOPT=OFF |
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- ) |
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- cmake-utils_src_configure |
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- |
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- # gentoo bug #302621 |
349 |
- has_version 'sci-libs/hdf5[mpi]' && export CXX=mpicxx CC=mpicc |
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-} |
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- |
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-src_compile() { |
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- cmake-utils_src_compile |
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- use doc && cmake-utils_src_compile -C doc |
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-} |
356 |
- |
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-src_install() { |
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- cmake-utils_src_install |
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- |
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- if use doc; then |
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- local i |
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- for i in lua octave python R ruby; do |
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- if use $i; then |
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- docinto html/${i,}_modular |
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- dodoc -r "${BUILD_DIR}"/src/interfaces/${i,}_modular/modshogun/doxygen_xml/. |
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- fi |
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- done |
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- fi |
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-} |