I have EGit 4.0 installed on Eclipse Mars (4.5.0). When I try to clone a project from GitHub I always get an error when I get to the "Source Git Repository" dialogue. As soon as I copy in the repository URL, I get the message "Internal error; consult Eclipse error log."
I reported this problem as bug 471813. The bug report was promptly closed with this message from Andrey Loskutov:
Sorry, not Eclipse issue: "Unable to locate secure storage module (com.aptana.ide.security.linux.provider)." Please contact Aptana devs for help.
However, I do not have Aptana installed on this Eclipse instance (nor in any other). Why is this problem being attributed to Aptana?
It is possible that you had/have aptana installed on another eclipse installation on the same machine. I had the same issue which I resolved by resetting my secure store. Preferences -> General -> Security -> Secure Storage -> Contents Tab.
Under the Contents Tab, you will see a list of secure stores on the left. Select the secure store and press the delete button on the right side.