A port is clashing with another program installed in /opt that is not a port

[Jerry]

Hi List,

Today I installed MacPorts into Lion 10.7.3. I used the pkg installer and then typed:

    sudo xcode-select -switch /Applications/Xcode.app

to expose Xcode 4.3.1

and then

    sudo port install py-spyder

(Spyder is a python IDE for technical computing.)

The installation failed with this error so that dbus and several other dependencies were not installed:

----------------------
Error: Target org.macports.activate returned: Image error: /Library/LaunchAgents/org.freedesktop.dbus-session.plist already exists and does not belong to a registered port.  Unable to activate port dbus. Use 'port -f activate dbus' to force the activation.
Error: Failed to install dbus
----------------------

I looked at /Library/LaunchAgents/org.freedesktop.dbus-session.plist and found that it is an alias that points to 

    /opt/openmodelica/Library/LaunchAgents/org.freedesktop.dbus-session.plist

It turns that I had some time back installed Open Modelica using a .mpkg from a .dmg downloaded from http://openmodelica.org/, so that my /opt at the upper levels looks like this:

    /opt/local
    /opt/openmodelica

If I take the suggestion by the MacPorts error message above to use 'port -f activate dbus' will this disturb anything with my Open Modelica installation?

Thanks,
Jerry