I am getting the following message everytime the PHP project based on Subversion loads...
Obviously shown, the OS is a Mac OSX Mountain Lion. I have also followed the instructions within the link, and it still appears at completely random times. However, subversion actions seem to work fine.
From main menu, select
Window -> Preferences -> Team -> SVN,
at right panel "SVN interface" zone.
You may find "client" is set to "JavaHL(JNI) Not Available".
Change it to "SVNKit(Pure Java) SVNKit vx.x"