spibou: Apart from the problems of version control and "dependency hell" when installing from source, the other main problem is that the apt package management system does not "know" about software installed by other methods.
As Ubuntu has periodic security updates for packages, the lack of version control with compiled software, and its dependencies, means that these can get out of sync with the packaged applications. This can lead to various problems, including system breakage.
I accept that it may be possible for an experienced user to resolve these problems, but IMHO this will be quite daunting to a newbie.
Bookmarks