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No engines loaded - Avogadro 1.03/1.2 for Linux


#1

Hi all,

Installed Avogadro 1.03 on Debian Jessie (Linux pc16851 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1 (2016-12-30) x86_64 GNU/Linux) via apt and the following wild error message appeared!

No engines loaded. It is unlikely this application will function correctly. Please correct this error.

An odd message appeared in the console:

"Avogadro version: 1.0.3 Git: LibAvogadro version: 1.2.0 Git: " Locale: "en_US" Libavogadro translations not found. "System has OpenGL support." "About to test OpenGL capabilities." "OpenGL capabilities found: " "Double Buffering." "Direct Rendering." "Antialiasing." PluginManager::setPluginPath() was not called from application - using default plugin path Loading plugins: "/usr/bin/../lib/avogadro/1_2" Loading plugins: "/home/taylorc/.avogadro/1_2/plugins" QStackedLayout::setCurrentWidget: Widget 0xc369c0 not contained in stack Settings are missing for the next engines: () GLWidget initialisation... GLWidget initialised... createObjects()

This directory does not exist. So, of course, the extensions menu is empty. Compiling 1.2 from tarball, largely the same result. The program loads but no extensions. Seems to have few issues when I install on my Linux Mint laptop so presumably there’s a dependency which is not satisfied or an incompatibility or so. I can’t attach files so excuse the output from cmake below. Maybe it has clues for the educated eyes on the forum. Please do let me know if there’s other information needed

Appreciate any help, cheers.

-- The C compiler identification is GNU 4.9.2 -- The CXX compiler identification is GNU 4.9.2 -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- 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 PkgConfig: /usr/bin/pkg-config (found version "0.28") -- checking for module 'openbabel-2.0>=2.3.0' -- found openbabel-2.0, version 2.3.2 -- Found OpenBabel 2.3 or later: openbabel -- Found OpenBabel2 executable: /usr/bin/babel -- Found Git revision is: -- Building released version. -- Searching for python dependencies... -- [1/5] Boost Python -- Boost version: 1.55.0 -- 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 "2.7.9") -- [4/5] Numpy Module -- Numpy headers found -- [5/5] SIP Module -- SIP version 266752 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 failed to create symbolic link '/home/taylorc/software/avogadro-1.2.0/build/libavogadro/include/avogadro//home/taylorc/software/avogadro-1.2.0/build/libavogadro/src/config.h': No such file or directory -- Enabled python terminal -- Found Qt4: /usr/bin/qmake (found suitable version "4.8.6", minimum required is "4.6") -- Linking in static plugins: bsdyengine;navigatetool;elementcolor -- Python site-packages directory: /usr/lib/python2.7/dist-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.8.8") -- 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:

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

LINK_INTERFACE_LIBRARIES:

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

– Generating done
– Build files have been written to: /home/taylorc/software/avogadro-1.2.0/build


#2

I’m not sure how you’re using the 1.0.3 version of the application with version 1.2.0 of the library.

They won’t find plugins because of the version mismatch.

I’m not sure what the issue installing from source is, but it looks like cmake worked OK. What happens when you build?

My one question about your cmake results is this line:
failed to create symbolic link '/home/taylorc/software/avogadro-1.2.0/build/libavogadro/include/avogadro//home/taylorc/software/avogadro-1.2.0/build/libavogadro/src/config.h': No such file or directory

It seems like you’ve got a circular symlink or a funny install prefix. How are you calling cmake?


#3

Howdy Geoff,

I’m literally following the INSTALL instructions from the 1.2 tarball so no special cmake options. Are there any I should be using?

Upon trying 1.03 first then uninstalling, I noticed the .avogadro file in my home and deleted it as apt didn’t, thought maybe it left behind some files that would clash with files from the 1.2 tarball but didn’t appear to make a difference.


#4

There’s clearly still a 1.0.3 binary around, or you wouldn’t get this message:

"Avogadro version: 1.0.3 Git:
LibAvogadro version: 1.2.0 Git: "

The other question is why nothing installed. If you ran “make install” it should, in principal, go into /usr/local instead of /home/taylorc

How are you running the newly-compiled-and-installed 1.2.0?