How to deal with configuration style warnings occuring from TexLive 2012 installation?

Solution 1:

Please have a look at the NEWS.Debian file. The following is from this file:

If you are using PostScript fonts that are not packaged for Debian, some changes have been done: updmap now reads all updmap.cfg files it finds. That means, the easiest way to activate local fonts (in TEXMFLOCAL) by putting the respective map lines into /usr/local/share/texmf/web2c/updmap.cfg, and call updmap-sys once (as root). If you have fonts in your home directory you want to activate, paralleling the above you put the respective map line into $HOME/texmf/web2c/updmap.cfg and call updmap (as user). But be reminded that you have to do that everytime system fonts have changed (there is no automatic syncronization between user specific and system wide updmap(-sys) generated files).

In your case it should be sufficient to install the latest version of lmodern, which is 2.004.2-1 for Quantal. After that you run update-updmap and the warnung should disappear.