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I am trying to get ClassicThesis to work with Lyx. Installed the Bera and Mathpazo fonts in my local texmf tree and ran updmap:

~/texmf/bera/dvips/config$ sudo updmap --enable Map bera.map
[sudo] password for <username>: 
updmap: This is updmap, version $Id: updmap 14402 2009-07-23 17:09:15Z karl $
updmap: using transcript file `/home/<username>/.texmf-var/web2c/updmap.log'
updmap: initial config file is `/var/lib/texmf/web2c/updmap.cfg'

However: when compiling the same error keeps popping up: !pdfTeX error: pdflatex (file fvmro8r): Font fvmro8r at 558 not found

I'm running texlive2009 on Ubuntu 12.04 icm Lyx 2.0.0

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Never use updmap along with sudo, for you're defining a map that's used only by root. Change updmap to updmap-sys – egreg May 17 '12 at 11:51
@egreg Please consider making your comment an answer. – Joseph Wright Aug 6 '12 at 20:57

The updmap script makes map files that are available only to the user who is issuing the command. Therefore

sudo updmap --enable Map bera.map

will produce map files valid for the user root. On some systems the map files might be stored in the "real" user home (from the transcript this can be the case for Ubuntu); however the file will probably not be readable without administrator privileges.

Always issue

sudo updmap-sys

for enabling new map files.

You should also remove the files created inside ~/.texmf-var.

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