Patch is atached.
Anton
diff -Nru avogadro-1.0.3/debian/changelog avogadro-1.0.3/debian/changelog
--- avogadro-1.0.3/debian/changelog 2013-06-02 14:55:23.000000000 +0200
+++ avogadro-1.0.3/debian/changelog 2013-11-03 16:28:22.000000000 +0100
@@ -1,3 +1,10 @@
+avogadro (1.0.3-10.1) unstable; urgency=low
+
+ * Non-maintainer upload.
+ * Replace eigen2 by eigen3. (Closes: #728610)
+
+ -- Anton Gladky <gl...@debian.org> Sun, 03 Nov 2013 16:28:19 +0100
+
avogadro (1.0.3-10) unstable; urgency=low
[ Daniel Leidert ]
diff -Nru avogadro-1.0.3/debian/control avogadro-1.0.3/debian/control
--- avogadro-1.0.3/debian/control 2013-06-01 23:28:13.000000000 +0200
+++ avogadro-1.0.3/debian/control 2013-10-30 15:17:37.000000000 +0100
@@ -6,7 +6,7 @@
Build-Depends: cmake (>> 2.6.0),
debhelper (>> 7.0.50~),
libboost-python-dev,
- libeigen2-dev (>> 2.0~beta6),
+ libeigen3-dev,
libgl2ps-dev,
libglew-dev,
libopenbabel-dev (>> 2.2.0),
diff -Nru avogadro-1.0.3/debian/patches/eigen3.patch avogadro-1.0.3/debian/patches/eigen3.patch
--- avogadro-1.0.3/debian/patches/eigen3.patch 1970-01-01 01:00:00.000000000 +0100
+++ avogadro-1.0.3/debian/patches/eigen3.patch 2013-11-03 16:27:26.000000000 +0100
@@ -0,0 +1,186 @@
+Description: migrate from eigen2 to eigen3
+Applied-Upstream: https://github.com/cryos/avogadro/commit/3cc14da0f92e6ea0bd763e97b5711c4afe56a7cd
+Author: Anton Gladky <gl...@debian.org>
+Bug-Debian: http://bugs.debian.org/728610
+Last-Update: 2013-11-03
+
+--- a/avogadro.prf.in
++++ b/avogadro.prf.in
+@@ -3,6 +3,6 @@
+ INCLUDEPATH += . \
+ $$AVOGADRO_PREFIX/include \
+ @OPENBABEL2_INCLUDE_DIR@ \
+- @EIGEN2_INCLUDE_DIR@
++ @EIGEN3_INCLUDE_DIR@
+ LIBS += -L$$AVOGADRO_PREFIX/lib -lavogadro \
+ -L$$OPENBABEL_PREFIX/lib -lopenbabel
+--- a/avogadro/src/CMakeLists.txt
++++ b/avogadro/src/CMakeLists.txt
+@@ -19,7 +19,7 @@
+ include_directories(
+ ${CMAKE_CURRENT_SOURCE_DIR}
+ ${OPENBABEL2_INCLUDE_DIR}
+- ${EIGEN2_INCLUDE_DIR}
++ ${EIGEN3_INCLUDE_DIR}
+ ${CMAKE_CURRENT_BINARY_DIR}
+ )
+
+--- a/cmake/modules/AvogadroUse.cmake
++++ b/cmake/modules/AvogadroUse.cmake
+@@ -16,8 +16,9 @@
+
+ # Add the Avogadro modules directory to the CMake module path
+ set(CMAKE_MODULE_PATH ${Avogadro_PLUGIN_DIR}/cmake ${CMAKE_MODULE_PATH})
+-find_package(Eigen2 REQUIRED)
+-include_directories(${EIGEN2_INCLUDE_DIR})
++find_package(Eigen3 REQUIRED)
++include_directories(${EIGEN3_INCLUDE_DIR})
++add_definitions(-DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API)
+ if(Avogadro_ENABLE_GLSL)
+ find_package(GLEW)
+ if(GLEW_FOUND)
+--- /dev/null
++++ b/cmake/modules/FindEigen3.cmake
+@@ -0,0 +1,81 @@
++# - Try to find Eigen3 lib
++#
++# This module supports requiring a minimum version, e.g. you can do
++# find_package(Eigen3 3.1.2)
++# to require version 3.1.2 or newer of Eigen3.
++#
++# Once done this will define
++#
++# EIGEN3_FOUND - system has eigen lib with correct version
++# EIGEN3_INCLUDE_DIR - the eigen include directory
++# EIGEN3_VERSION - eigen version
++
++# Copyright (c) 2006, 2007 Montel Laurent, <mon...@kde.org>
++# Copyright (c) 2008, 2009 Gael Guennebaud, <g.g...@free.fr>
++# Copyright (c) 2009 Benoit Jacob <jacob.benoi...@gmail.com>
++# Redistribution and use is allowed according to the terms of the 2-clause BSD license.
++
++if(NOT Eigen3_FIND_VERSION)
++ if(NOT Eigen3_FIND_VERSION_MAJOR)
++ set(Eigen3_FIND_VERSION_MAJOR 2)
++ endif(NOT Eigen3_FIND_VERSION_MAJOR)
++ if(NOT Eigen3_FIND_VERSION_MINOR)
++ set(Eigen3_FIND_VERSION_MINOR 91)
++ endif(NOT Eigen3_FIND_VERSION_MINOR)
++ if(NOT Eigen3_FIND_VERSION_PATCH)
++ set(Eigen3_FIND_VERSION_PATCH 0)
++ endif(NOT Eigen3_FIND_VERSION_PATCH)
++
++ set(Eigen3_FIND_VERSION "${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
++ ${KDE4_INCLUDE_DIR}
++ PATH_SUFFIXES eigen3 eigen
++ )
++
++ if(EIGEN3_INCLUDE_DIR)
++ _eigen3_check_version()
++ endif(EIGEN3_INCLUDE_DIR)
++
++ include(FindPackageHandleStandardArgs)
++ find_package_handle_standard_args(Eigen3 DEFAULT_MSG EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
++
++ mark_as_advanced(EIGEN3_INCLUDE_DIR)
++
++endif(EIGEN3_INCLUDE_DIR)
++
+--- a/libavogadro/src/CMakeLists.txt
++++ b/libavogadro/src/CMakeLists.txt
+@@ -14,7 +14,7 @@
+ "${libavogadro_BINARY_DIR}/include;${tmp_include_dirs}")
+ include_directories(
+ ${CMAKE_CURRENT_BINARY_DIR}
+- ${EIGEN2_INCLUDE_DIR}
++ ${EIGEN3_INCLUDE_DIR}
+ ${OPENBABEL2_INCLUDE_DIR}
+ )
+
+--- a/libavogadro/tests/CMakeLists.txt
++++ b/libavogadro/tests/CMakeLists.txt
+@@ -14,7 +14,7 @@
+ include_directories(
+ ${CMAKE_SOURCE_DIR}
+ ${CMAKE_CURRENT_BINARY_DIR}
+- ${EIGEN2_INCLUDE_DIR}
++ ${EIGEN3_INCLUDE_DIR}
+ ${OPENBABEL2_INCLUDE_DIR}
+ ${BOOST_PYTHON_INCLUDES}
+ ${PYTHON_INCLUDE_PATH}
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -192,7 +192,7 @@
+ find_package(Qt4 REQUIRED) # find and setup Qt4 for this project
+ find_package(OpenGL REQUIRED) # find and setup OpenGL
+ find_package(Linguist) # find and setup Linguist
+-find_package(Eigen2 REQUIRED) # find and setup Eigen2
++find_package(Eigen3 REQUIRED) # find and setup Eigen3
+ find_package(ZLIB REQUIRED)
+ find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel
+
+@@ -427,7 +427,7 @@
+
+ # Install the find modules we require to be present
+ install(FILES
+- "${CMAKE_MODULE_PATH}/FindEigen2.cmake"
++ "${CMAKE_MODULE_PATH}/FindEigen3.cmake"
+ "${CMAKE_MODULE_PATH}/FindGLEW.cmake"
+ DESTINATION "${Avogadro_PLUGIN_INSTALL_DIR}/cmake")
+
+--- a/libavogadro/CMakeLists.txt
++++ b/libavogadro/CMakeLists.txt
+@@ -3,6 +3,7 @@
+ # We probably want to adopt the libtool scheme once we hit 1.0.0
+ set(SOVERSION 0)
+
++add_definitions(-DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API)
+ if (WIN32)
+ add_definitions( -DWIN32 )
+ # add definitions for OB in WIN32
+--- a/avogadro/CMakeLists.txt
++++ b/avogadro/CMakeLists.txt
+@@ -6,5 +6,6 @@
+ add_definitions( -DUSING_OBDLL -DUSING_DYNAMIC_LIBS )
+ endif (WIN32)
+
++add_definitions(-DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API)
+ # tell cmake to process CMakeLists.txt in that subdirectory
+ add_subdirectory(src)
diff -Nru avogadro-1.0.3/debian/patches/series avogadro-1.0.3/debian/patches/series
--- avogadro-1.0.3/debian/patches/series 2013-06-02 14:54:39.000000000 +0200
+++ avogadro-1.0.3/debian/patches/series 2013-10-30 15:14:50.000000000 +0100
@@ -2,3 +2,4 @@
nwchem_input_ccsd.patch
boost148.patch
hurd_ftbfs.patch
+eigen3.patch
diff -Nru avogadro-1.0.3/debian/source/include-binaries avogadro-1.0.3/debian/source/include-binaries
--- avogadro-1.0.3/debian/source/include-binaries 1970-01-01 01:00:00.000000000 +0100
+++ avogadro-1.0.3/debian/source/include-binaries 2013-10-30 15:27:06.000000000 +0100
@@ -0,0 +1,4 @@
+obj-x86_64-linux-gnu/CMakeFiles/2.8.11.2/CMakeDetermineCompilerABI_C.bin
+obj-x86_64-linux-gnu/CMakeFiles/2.8.11.2/CMakeDetermineCompilerABI_CXX.bin
+obj-x86_64-linux-gnu/CMakeFiles/2.8.11.2/CompilerIdC/a.out
+obj-x86_64-linux-gnu/CMakeFiles/2.8.11.2/CompilerIdCXX/a.out
