As always, it depends. This is one of the potential problems when installing from source, the names and locations of libraries and binaries can conflict between apt (apt-get) and sudo make install
There are 2 general solutions:
First - Installing source code into /usr/local
- minimizes conflicts with system files in /usr
This is what I generally do
./configure --prefix=/usr/local
make
sudo make install
Second - Probably better, use check install
sudo apt-get install checkinstall
./configure
make
sudo checkinstall
This makes a .deb from your source code and thus works better with apt
. The package can then be installed and removed similar to any other .deb.
See https://help.ubuntu.com/community/CompilingEasyHowTo
You would then put the package on hold
see How to prevent updating of a specific package?
and then update the package, manually downloading the source code and re-compiling (with checkinstall) or taking it off hold and using the ubuntu repositories (apt).
Note: IMO installing into /usr/local is LEAST likely to result in problems with system files as it is cleaner (keeps the source files and system files completely separate). checkinstall is very relilable, but, if there is a conflict you can break the system.