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 <gl...@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 <gl...@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, <mon...@kde.org> ++# Copyright (c) 2008, 2009 Gael Guennebaud, <g.g...@free.fr> ++# Copyright (c) 2009 Benoit Jacob <jacob.benoi...@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
