[Openchemistry-users] Problem with Avogadro 2 build on OSX

Marcus D. Hanwell marcus.hanwell at kitware.com
Thu Mar 10 11:21:07 EST 2016

Hi Marc,

On Wed, Mar 9, 2016 at 8:57 PM, Marc-André Dubois
<marc-andre.dubois at polymtl.ca> wrote:
> Hi,
>    I am a long time user of Avogadro. I recently saw Open Chemistry with Avogadro 2 and Molequeue and I really want to use the project for my work. However, I had a lot of trouble building the apps. I am currently running osx 10.7.5, osx 10.11.x and Ubuntu (not tested yet). The state of the build is the following:
> on osx 10.7.5:
>         Molequeue: Built and installed (fully functional)
>         Avogadrolibs: Built and installed
>         Avogadroapp: Build incomplete... I have a linking problem. Here is my output:
> [100%] Linking CXX executable ../bin/Avogadro2.app/Contents/MacOS/Avogadro2
> Undefined symbols for architecture x86_64:
<snip - many missing symbols>
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> make[2]: *** [bin/Avogadro2.app/Contents/MacOS/Avogadro2] Error 1
> make[1]: *** [avogadro/CMakeFiles/avogadro.dir/all] Error 2
> make: *** [all] Error 2
> As I understand, it look like some libraries are missing. Is there a connection between avogadrolibs and avogadroapp? When I prepare avogadrolibs with cmake, I get this warning:
> MACOSX_RPATH is not specified for the following targets:
>  AvogadroCore
>  AvogadroIO
>  AvogadroQuantumIO
Yes, avogadroapp depends on and requires avogadrolibs. If you go to
http://www.openchemistry.org/downloads/ you can get a Mac binary I
built recently for the 0.9.0 release. The Mac uses an app bundle, and
I use the openchemistry superbuild to coordinate building all the
> Avogadrolibs build just fine with my setup despite of this message, but is it possible, this could be the source of my linking problem? I tried to use the binaries directly, but those were compiled with a 10.8+ version of OSX so it does not work with my 10.7.5 osx, so I would prefer to build the apps myself instead. Thank you for your help.
Yes, we don't test on 10.7 any longer, and I am not sure if there will
be other issues there with Qt 5. The Avogadro application must link to
the Avogadro libraries, the linker error you see suggests that it is
not able to find the libraries correctly, if you can try,

VERBOSE=1 make -j1

It should show you the link line, and that may help me see what the
issue is. I can check out whether we could broaden support, but
http://doc.qt.io/qt-5/osx.html indicates limited support for OS less
recent than 10.8.



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