The texlive 2012 and the libertine font version (currently 5.3) has been already updated by:
Tlmgr update --all
However, I found texmaker pdflatex invoke libertine-legacy, because when using \usepackage[lining]{libertine} there is such an error:

but typing in terminal pdflatex filename.tex, no error arose. However, texmaker pdflatex will produce lining numbers without this option.
Another evidence is that the maths font is slightly different:
pdflatex in Terminal: superscript `f` is more close to the left Letter in math mode.

Texmaker pdflatex:

So how to make texmaker pdflatex loads the latest libertine font?

This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) (format=pdflatex 2012.11.19) 24 JAN 2013 12:06– KOF Jan 24 at 11:07bashrc. When opening texmaker in terminal, it loads the path and everything is ok. – KOF Jan 24 at 11:24bashrcbut in/etc/environment(make a backup first), append the path to/etc/environment, log out, log in, and someone is your uncle. – daleif Jan 24 at 11:30