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ghutchis / avogadro

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.
http://avogadro.cc/
GNU General Public License v2.0
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Cannot compile on Ubuntu 14.04, problem with <Eigen/Core> #716

Closed ghutchis closed 8 years ago

ghutchis commented 10 years ago

Dear Developers,

I'm trying to install the latest version, as described here (http://xtalopt.openmolecules.net/wiki/index.fcgi/wiki/Installation), and I think I have done everthing by the books. If anyone could help it would be tremedeously appreciated.

The cmake command mostly fairs well (see below), but has a few messages to the developers. When I then try to run make, it crashes complaining about "fatal error: Eigen/Core: No such file or directory

include <Eigen/Core>"

I'm running a Ubuntu 14.04 on an intel i5, all freshly installed. I am not familiar with what it is exactly, but I have installed both eigen2 and eigen3, and all other necessary dependancies (as far as I can tell), all using ubuntu's package manager. It's crucial I get it to work... argh.

Very thankful for help, Martin

martin@box:~/Programs/avogadro/build$ cmake .. -DOPENBABEL2_INCLUDE_DIR=$HOME/include/openbabel-2.0 -DOPENBABEL2_LIBRARIES=$HOME/lib/libopenbabel.so -DOPENBABEL2_VERSION_MET=true -DOPENBABEL_IS_NEWER_THAN_2_2_99=true -DCMAKE_INSTALL_PREFIX=$HOME -- The C compiler identification is GNU 4.8.2 -- The CXX compiler identification is GNU 4.8.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- The build type is RelWithDebInfo -- Performing Test HAVE_NO_RTTI -- Performing Test HAVE_NO_RTTI - Success -- Performing Test HAVE_RTTI -- Performing Test HAVE_RTTI - Success -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success -- Performing Test COMPILES_WITHOUT_FPERMISSIVE -- Performing Test COMPILES_WITHOUT_FPERMISSIVE - Failed -- Looking for Q_WS_X11 -- Looking for Q_WS_X11 - found -- Looking for Q_WS_WIN -- Looking for Q_WS_WIN - not found -- Looking for Q_WS_QWS -- Looking for Q_WS_QWS - not found -- Looking for Q_WS_MAC -- Looking for Q_WS_MAC - not found -- Found Qt4: /usr/bin/qmake (found suitable version "4.8.6", minimum required is "4.6.0") -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so -- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so
-- Found lupdate: /usr/bin/lupdate-qt4 -- Found lrelease: /usr/bin/lrelease-qt4 -- Found lconvert: /usr/bin/lconvert -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") -- Found OpenBabel2 executable: /home/martin/bin/babel -- Git revision found to be 3561ccf -- Found Git revision is: 3561ccf -- Building development version from Git clone. -- Searching for python dependencies... -- [1/5] Boost Python -- Boost version: 1.54.0 -- Found the following Boost libraries: -- python -- Boost Python found... -- [2/5] Python Libraries -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so
-- [3/5] Python Interpreter -- Found PythonInterp: /usr/bin/python (found version "2.7.6") -- [4/5] Numpy Module -- Numpy headers found -- [5/5] SIP Module -- SIP version 265989 found -- Found SIP: /usr/include/python2.7
-- All python dependencies found - Python support enabled -- Threaded OpenGL rendering not enabled -- RPath support enabled for installed binaries and libraries -- Setting new boost python libraries -- Enabled python terminal -- Found Qt4: /usr/bin/qmake (found suitable version "4.8.6", minimum required is "4.6") -- Found Eigen2: /usr/include/eigen2 (Required is at least version "2.0.0") -- Linking in static plugins: bsdyengine;navigatetool;elementcolor -- Python site-packages directory: /usr/lib/python2.7/dist-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.8.6") -- docbook tools not found, doc targets disabled -- Configuring done CMake Warning (dev) in libavogadro/src/CMakeLists.txt: Policy CMP0022 is not set: INTERFACE_LINK_LIBRARIES defines the link interface. Run "cmake --help-policy CMP0022" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

Target "avogadro" has an INTERFACE_LINK_LIBRARIES property which differs from its LINK_INTERFACE_LIBRARIES properties.

INTERFACE_LINK_LIBRARIES:

/home/martin/lib/libopenbabel.so;/usr/lib/x86_64-linux-gnu/libQtOpenGL.so;/usr/lib/x86_64-linux-gnu/libQtGui.so;/usr/lib/x86_64-linux-gnu/libQtCore.so;/usr/lib/x86_64-linux-gnu/libGLU.so;/usr/lib/x86_64-linux-gnu/libGL.so;/usr/lib/x86_64-linux-gnu/libSM.so;/usr/lib/x86_64-linux-gnu/libICE.so;/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so;/usr/lib/x86_64-linux-gnu/libpython2.7.so;/usr/lib/x86_64-linux-gnu/libboost_python.so;bsdyengine;navigatetool;elementcolor

LINK_INTERFACE_LIBRARIES:

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) in libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt: Policy CMP0022 is not set: INTERFACE_LINK_LIBRARIES defines the link interface. Run "cmake --help-policy CMP0022" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

Target "OpenQube" has an INTERFACE_LINK_LIBRARIES property which differs from its LINK_INTERFACE_LIBRARIES properties.

INTERFACE_LINK_LIBRARIES:

$<$<NOT:$<CONFIG:DEBUG>>:/usr/lib/x86_64-linux-gnu/libQtCore.so>;$<$<CONFIG:DEBUG>:/usr/lib/x86_64-linux-gnu/libQtCore.so>

LINK_INTERFACE_LIBRARIES:

This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done CMake Warning: Manually-specified variables were not used by the project:

OPENBABEL_IS_NEWER_THAN_2_2_99

-- Build files have been written to: /home/martin/Programs/avogadro/build

martin@box:~/Programs/avogadro/build$ make -j3 [ 0%] [ 0%] [ 0%] Generating ui_bsdysettingswidget.h Generating moc_elementcolor.cxx Generating qrc_navigatetool.cxx [ 1%] [ 1%] Generating moc_bsdyengine.cxx Generating moc_navigatetool.cxx Scanning dependencies of target elementcolor [ 1%] Generating ui_navigatesettingswidget.h [ 1%] Scanning dependencies of target bsdyengine Scanning dependencies of target navigatetool Building CXX object libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o [ 1%] [ 1%] Building CXX object libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o Building CXX object libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o In file included from /home/martin/Programs/avogadro/libavogadro/src/colors/elementcolor.cpp:27:0: /home/martin/Programs/avogadro/build/libavogadro/include/avogadro/primitive.h:34:22: fatal error: Eigen/Core: No such file or directory

include <Eigen/Core>

                  ^

compilation terminated. In file included from /home/martin/Programs/avogadro/libavogadro/src/tools/navigatetool.h:29:0, from /home/martin/Programs/avogadro/libavogadro/src/tools/navigatetool.cpp:26: /home/martin/Programs/avogadro/build/libavogadro/include/avogadro/glwidget.h:32:22: fatal error: Eigen/Core: No such file or directory

include <Eigen/Core>

                  ^

compilation terminated. In file included from /home/martin/Programs/avogadro/build/libavogadro/include/avogadro/primitivelist.h:29:0, from /home/martin/Programs/avogadro/build/libavogadro/include/avogadro/engine.h:37, from /home/martin/Programs/avogadro/libavogadro/src/engines/bsdyengine.h:29, from /home/martin/Programs/avogadro/libavogadro/src/engines/bsdyengine.cpp:25: /home/martin/Programs/avogadro/build/libavogadro/include/avogadro/primitive.h:34:22: fatal error: Eigen/Core: No such file or directory

include <Eigen/Core>

                  ^

compilation terminated. make[2]: * [libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o] Error 1 make[1]: * [libavogadro/src/colors/CMakeFiles/elementcolor.dir/all] Error 2 make[1]: * Waiting for unfinished jobs.... [ 1%] Building CXX object libavogadro/src/engines/CMakeFiles/bsdyengine.dir/moc_bsdyengine.cxx.o make[2]: * [libavogadro/src/tools/CMakeFiles/navigatetool.dir/navigatetool.cpp.o] Error 1 make[1]: *\ [libavogadro/src/tools/CMakeFiles/navigatetool.dir/all] Error 2 In file included from /home/martin/Programs/avogadro/build/libavogadro/include/avogadro/primitivelist.h:29:0, from /home/martin/Programs/avogadro/build/libavogadro/include/avogadro/engine.h:37, from /home/martin/Programs/avogadro/build/libavogadro/src/engines/../../../../libavogadro/src/engines/bsdyengine.h:29, from /home/martin/Programs/avogadro/build/libavogadro/src/engines/moc_bsdyengine.cxx:9: /home/martin/Programs/avogadro/build/libavogadro/include/avogadro/primitive.h:34:22: fatal error: Eigen/Core: No such file or directory

include <Eigen/Core>

                  ^

compilation terminated. make[2]: * [libavogadro/src/engines/CMakeFiles/bsdyengine.dir/bsdyengine.cpp.o] Error 1 make[2]: * Waiting for unfinished jobs.... make[2]: * [libavogadro/src/engines/CMakeFiles/bsdyengine.dir/moc_bsdyengine.cxx.o] Error 1 make[1]: * [libavogadro/src/engines/CMakeFiles/bsdyengine.dir/all] Error 2 make: *\ [all] Error 2

Reported by: *anonymous

ghutchis commented 10 years ago

After replacing eigen3 with eigen2, the make proceeds 12 %, until after setup of Openqube.

Linking CXX shared library ../../../../../lib/libavogadro_OpenQube.so [ 12%] Built target OpenQube make: *\ [all] Error 2

I think it comes down to this error shown by cmake:

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) in libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt: Policy CMP0022 is not set: INTERFACE_LINK_LIBRARIES defines the link interface. Run "cmake --help-policy CMP0022" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

Target "OpenQube" has an INTERFACE_LINK_LIBRARIES property which differs from its LINK_INTERFACE_LIBRARIES properties.

INTERFACE_LINK_LIBRARIES:

$<$<NOT:$<CONFIG:DEBUG>>:/usr/lib/x86_64-linux-gnu/libQtCore.so>;$<$<CONFIG:DEBUG>:/usr/lib/x86_64-linux-gnu/libQtCore.so>

LINK_INTERFACE_LIBRARIES:

Can this be made to work somehow?

I would be very grateful, Martin

Original comment by: *anonymous