0
sudo apt-get install php5-xdebug
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
  php5-xdebug: Depends: phpapi-20060613
E: Broken packages
tchalvak:~/sites/loltrading$ apt-cache show phpapi-20060613

Is there any way to get around this and run xdebug with php 5.3 on ubuntu?

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Where did you get your custom version of php, did you build that yourself? You will probably have to build a custom php5-xdebug package as well. If you built your own php it should be pretty easy to get the source package for xdebug and rebuild it against your custom php.

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