Common Issues
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In "98%" of cases, the issue you're having is one of the following:
Program doesn't start
Run the program from terminal to see errors if the app doesn't work as intended. Note however that program authors doesn't always purge their programs of warnings on console, so make sure what you're seeing is relevant and a real error.
Shared libraries errors
One of the errormsgs you will see when starting an app from terminal is something called a shared library error and they usually look like this:
"someapp: error while loading shared libraries: libfoo.so.1: cannot open shared object file: No such file or directory"
The recommended way to fix this is to rebuild the librarie(s)/application(s)[*ABS]. However, you will find lots of people ready to tell you to just symlink one version of a library with another. This is not recommended. The reason it's not recommended is because this can cause problems when a fixed package is pushed to repo and cause false bugreports for the developers to deal with. It may also give you unstable behaviour and unintended behaviour & crashes. However, this is the only option for applications which you don't have the sourcecode for.
Program doesn't work as intended and/or doesn't start
Rename or delete ~/.nameofprogram (and now because of new FreeDesktop.org standards, you should also check ~/.config/nameofprogram). Also there is something called ~/.local.
usually, if you're smart, you can also get away with renaming or deleting just a certain file inside the settingsdir and sometimes, just modify a textfile.
example(fixed the qt 4.5.1 upgrade and kde 4.2.2 issues [1]):
rm ~/.kde4/cache-* rm ~/.kde/cache-*/kpc/plasma*
Still doesn't work
If an app just plainly doesn't work and you have checked all of the above, usually upping the package version, removing patches, adding patches, removing/adding configure options in a logical way, is the way to go[*ABS]. In my personal experience(but that doesn't mean it's universal) the usual problems were because of unecessary patches and long unnecessary configure option lines. Other people may also experience the same problems as you, so a bugtracker search and/or forumsearch would be pertinent at this point.