Under gentoo, the libertine font package may be installed using the sunrise overlay. If you prefer updating your local texmf by hand, you may obtain errors like these when executing the commands in missfont.log:
$ mktexpk --mfmode / --bdpi 600 --mag 0+480/600 --dpi 480 LinLibertineT-tlf-sc-t1--base mktexpk: don't know how to create bitmap font for LinLibertineT-tlf-sc-t1--base. mktexpk: perhaps LinLibertineT-tlf-sc-t1--base is missing from the map file.
What you should do then is checking for a disabled map file. If updmap gives this result,
$ updmap --listmaps | grep libertine #! Map libertine.map
then the map file has to be enabled.
$ updmap --enable Map libertine.map
With a result like this, everything should work fine.
$ updmap --listmaps | grep libertine Map libertine.map