Bug#728324: Patch
The patch is attached.
Anton
diff -Nru kalzium-4.10.5/debian/changelog kalzium-4.10.5/debian/changelog
--- kalzium-4.10.5/debian/changelog 2013-07-12 17:02:20.000000000 +0200
+++ kalzium-4.10.5/debian/changelog 2013-10-30 18:30:12.000000000 +0100
@@ -1,3 +1,10 @@
+kalzium (4:4.10.5-1.1) unstable; urgency=low
+
+ * Non-maintainer upload.
+ * Replace eigen2 by eigen3. (Closes: #728324)
+
+ -- Anton Gladky <gladk@debian.org> Wed, 30 Oct 2013 18:30:06 +0100
+
kalzium (4:4.10.5-1) unstable; urgency=low
* New upstream release.
diff -Nru kalzium-4.10.5/debian/control kalzium-4.10.5/debian/control
--- kalzium-4.10.5/debian/control 2013-07-12 17:02:20.000000000 +0200
+++ kalzium-4.10.5/debian/control 2013-10-30 18:31:51.000000000 +0100
@@ -12,7 +12,7 @@
libboost-python-dev,
libfacile-ocaml-dev,
libopenbabel-dev, pkg-config,
- libeigen2-dev (>> 2.0.3),
+ libeigen3-dev,
libavogadro-dev,
libglew-dev,
libsm-dev
diff -Nru kalzium-4.10.5/debian/patches/eigen3.patch kalzium-4.10.5/debian/patches/eigen3.patch
--- kalzium-4.10.5/debian/patches/eigen3.patch 1970-01-01 01:00:00.000000000 +0100
+++ kalzium-4.10.5/debian/patches/eigen3.patch 2013-10-30 18:32:32.000000000 +0100
@@ -0,0 +1,186 @@
+Description: migrate from eigen2 to eigen3
+Author: Anton Gladky <gladk@debian.org>
+Bug-Debian: http://bugs.debian.org/728324
+Last-Update: 2013-10-13
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -30,7 +30,7 @@
+
+ include(KalziumConfigureChecks.cmake)
+
+-if (OPENBABEL2_FOUND AND Avogadro_FOUND AND EIGEN2_FOUND)
++if (OPENBABEL2_FOUND AND Avogadro_FOUND AND EIGEN3_FOUND)
+ # avoid compilerwarnings about redefinitions
+ # todo: use check_function_exits() ?
+ message(STATUS "Kalzium molecular editor enabled")
+@@ -38,9 +38,9 @@
+ add_definitions(-DHAVE_SNPRINTF -DHAVE_STRCASECMP -DHAVE_STRNCASECMP)
+ endif (WIN32)
+ add_subdirectory(compoundviewer)
+-else (OPENBABEL2_FOUND AND Avogadro_FOUND AND EIGEN2_FOUND)
++else (OPENBABEL2_FOUND AND Avogadro_FOUND AND EIGEN3_FOUND)
+ message(STATUS "Kalzium molecular editor disabled")
+-endif (OPENBABEL2_FOUND AND Avogadro_FOUND AND EIGEN2_FOUND)
++endif (OPENBABEL2_FOUND AND Avogadro_FOUND AND EIGEN3_FOUND)
+
+ add_subdirectory(doc)
+ add_subdirectory(src)
+--- /dev/null
++++ b/cmake/modules/FindEigen3.cmake
+@@ -0,0 +1,81 @@
++# - Try to find Eigen3 lib
++#
++# This module supports requiring a minimum version, e.g. you can do
++# find_package(Eigen3 3.1.2)
++# to require version 3.1.2 or newer of Eigen3.
++#
++# Once done this will define
++#
++# EIGEN3_FOUND - system has eigen lib with correct version
++# EIGEN3_INCLUDE_DIR - the eigen include directory
++# EIGEN3_VERSION - eigen version
++
++# Copyright (c) 2006, 2007 Montel Laurent, <montel@kde.org>
++# Copyright (c) 2008, 2009 Gael Guennebaud, <g.gael@free.fr>
++# Copyright (c) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
++# Redistribution and use is allowed according to the terms of the 2-clause BSD license.
++
++if(NOT Eigen3_FIND_VERSION)
++ if(NOT Eigen3_FIND_VERSION_MAJOR)
++ set(Eigen3_FIND_VERSION_MAJOR 2)
++ endif(NOT Eigen3_FIND_VERSION_MAJOR)
++ if(NOT Eigen3_FIND_VERSION_MINOR)
++ set(Eigen3_FIND_VERSION_MINOR 91)
++ endif(NOT Eigen3_FIND_VERSION_MINOR)
++ if(NOT Eigen3_FIND_VERSION_PATCH)
++ set(Eigen3_FIND_VERSION_PATCH 0)
++ endif(NOT Eigen3_FIND_VERSION_PATCH)
++
++ set(Eigen3_FIND_VERSION "${Eigen3_FIND_VERSION_MAJOR}.${Eigen3_FIND_VERSION_MINOR}.${Eigen3_FIND_VERSION_PATCH}")
++endif(NOT Eigen3_FIND_VERSION)
++
++macro(_eigen3_check_version)
++ file(READ "${EIGEN3_INCLUDE_DIR}/Eigen/src/Core/util/Macros.h" _eigen3_version_header)
++
++ string(REGEX MATCH "define[ \t]+EIGEN_WORLD_VERSION[ \t]+([0-9]+)" _eigen3_world_version_match "${_eigen3_version_header}")
++ set(EIGEN3_WORLD_VERSION "${CMAKE_MATCH_1}")
++ string(REGEX MATCH "define[ \t]+EIGEN_MAJOR_VERSION[ \t]+([0-9]+)" _eigen3_major_version_match "${_eigen3_version_header}")
++ set(EIGEN3_MAJOR_VERSION "${CMAKE_MATCH_1}")
++ string(REGEX MATCH "define[ \t]+EIGEN_MINOR_VERSION[ \t]+([0-9]+)" _eigen3_minor_version_match "${_eigen3_version_header}")
++ set(EIGEN3_MINOR_VERSION "${CMAKE_MATCH_1}")
++
++ set(EIGEN3_VERSION ${EIGEN3_WORLD_VERSION}.${EIGEN3_MAJOR_VERSION}.${EIGEN3_MINOR_VERSION})
++ if(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
++ set(EIGEN3_VERSION_OK FALSE)
++ else(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
++ set(EIGEN3_VERSION_OK TRUE)
++ endif(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
++
++ if(NOT EIGEN3_VERSION_OK)
++
++ message(STATUS "Eigen3 version ${EIGEN3_VERSION} found in ${EIGEN3_INCLUDE_DIR}, "
++ "but at least version ${Eigen3_FIND_VERSION} is required")
++ endif(NOT EIGEN3_VERSION_OK)
++endmacro(_eigen3_check_version)
++
++if (EIGEN3_INCLUDE_DIR)
++
++ # in cache already
++ _eigen3_check_version()
++ set(EIGEN3_FOUND ${EIGEN3_VERSION_OK})
++
++else (EIGEN3_INCLUDE_DIR)
++
++ find_path(EIGEN3_INCLUDE_DIR NAMES signature_of_eigen3_matrix_library
++ PATHS
++ ${CMAKE_INSTALL_PREFIX}/include
++ ${KDE4_INCLUDE_DIR}
++ PATH_SUFFIXES eigen3 eigen
++ )
++
++ if(EIGEN3_INCLUDE_DIR)
++ _eigen3_check_version()
++ endif(EIGEN3_INCLUDE_DIR)
++
++ include(FindPackageHandleStandardArgs)
++ find_package_handle_standard_args(Eigen3 DEFAULT_MSG EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
++
++ mark_as_advanced(EIGEN3_INCLUDE_DIR)
++
++endif(EIGEN3_INCLUDE_DIR)
++
+--- a/compoundviewer/CMakeLists.txt
++++ b/compoundviewer/CMakeLists.txt
+@@ -2,7 +2,7 @@
+
+ include_directories(
+ ${CMAKE_CURRENT_BINARY_DIR}/..
+- ${EIGEN2_INCLUDE_DIR}
++ ${EIGEN3_INCLUDE_DIR}
+ ${OPENBABEL2_INCLUDE_DIR}
+ )
+
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -23,7 +23,7 @@
+ )
+ include_directories(${OPENBABEL2_INCLUDE_DIR})
+
+- if (EIGEN2_FOUND AND Avogadro_FOUND)
++ if (EIGEN3_FOUND AND Avogadro_FOUND)
+
+ include(${Avogadro_USE_FILE})
+
+@@ -35,8 +35,8 @@
+ kde4_add_ui_files(kalziumtools_SRCS
+ tools/moleculeviewerwidget.ui
+ )
+- include_directories(${EIGEN2_INCLUDE_DIR})
+- endif (EIGEN2_FOUND AND Avogadro_FOUND)
++ include_directories(${EIGEN3_INCLUDE_DIR})
++ endif (EIGEN3_FOUND AND Avogadro_FOUND)
+ endif (OPENBABEL2_FOUND)
+
+ ## Kalzium calculator files
+@@ -138,9 +138,9 @@
+
+ if (OPENBABEL2_FOUND)
+ target_link_libraries(kalzium ${OPENBABEL2_LIBRARIES})
+- if (EIGEN2_FOUND AND Avogadro_FOUND)
++ if (EIGEN3_FOUND AND Avogadro_FOUND)
+ target_link_libraries(kalzium ${QT_QTOPENGL_LIBRARY} compoundviewer avogadro)
+- endif (EIGEN2_FOUND AND Avogadro_FOUND)
++ endif (EIGEN3_FOUND AND Avogadro_FOUND)
+ endif (OPENBABEL2_FOUND)
+
+ if (LIBFACILE_FOUND)
+--- a/KalziumConfigureChecks.cmake
++++ b/KalziumConfigureChecks.cmake
+@@ -4,7 +4,7 @@
+ macro_optional_find_package(OCaml)
+ macro_optional_find_package(Libfacile)
+ macro_optional_find_package(OpenBabel2)
+-macro_optional_find_package(Eigen2)
++macro_optional_find_package(Eigen3)
+ macro_optional_find_package(Avogadro 1.0.0 NO_MODULE)
+
+ find_package(PkgConfig)
+@@ -14,7 +14,7 @@
+
+ macro_bool_to_01(LIBFACILE_FOUND HAVE_FACILE)
+ macro_bool_to_01(OPENBABEL2_FOUND HAVE_OPENBABEL2)
+-macro_bool_to_01(EIGEN2_FOUND HAVE_EIGEN)
++macro_bool_to_01(EIGEN3_FOUND HAVE_EIGEN)
+ macro_bool_to_01(Avogadro_FOUND HAVE_AVOGADRO)
+
+ # at the end, output the configuration
+@@ -26,7 +26,7 @@
+ macro_log_feature(OCAML_FOUND "OCaml" "OCaml is needed by Kalzium for the Equation Solver" "http://caml.inria.fr/"; FALSE "" "")
+ macro_log_feature(LIBFACILE_FOUND "LibFacile" "libfacile is needed by Kalzium for the Equation Solver." "http://www.recherche.enac.fr/log/facile/"; FALSE "" "")
+ macro_log_feature(OPENBABEL2_FOUND "OpenBabel2" "OpenBabel is needed by Kalzium for the 3D-molecule viewer" "http://openbabel.sourceforge.net/"; FALSE "2.2" "")
+-macro_log_feature(EIGEN2_FOUND "Eigen2" "A generic C++ template library for dense and sparse matrices" "http://eigen.tuxfamily.org"; FALSE "2.0.0" "")
++macro_log_feature(EIGEN3_FOUND "Eigen3" "A generic C++ template library for dense and sparse matrices" "http://eigen.tuxfamily.org"; FALSE "2.0.0" "")
+ macro_log_feature(Avogadro_FOUND "Avogadro" "Advanced molecular editor" "http://avogadro.openmolecules.net"; FALSE "1.0" "")
+ macro_log_feature(CHEMICAL_MIME_DATA_FOUND "Chemical mime data" "Needed to open CML molecules from the file manager" "http://chemical-mime.sourceforge.net/"; FALSE "" "")
+
diff -Nru kalzium-4.10.5/debian/patches/series kalzium-4.10.5/debian/patches/series
--- kalzium-4.10.5/debian/patches/series 2013-07-12 17:02:20.000000000 +0200
+++ kalzium-4.10.5/debian/patches/series 2013-10-30 18:32:35.000000000 +0100
@@ -1 +1,2 @@
no_install_rpath_use_link_path.diff
+eigen3.patch
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