I believe I am seeing this same problem on an SVN checkout of trunk (4.6.2) 
with Ubuntu 12.04.2 LTS.

Validation/DiscriminateFunction/Comet/CometDiscrimValMixtureDistr.cxx: In 
constructor ‘CometDiscrimValMixtureDistr::CometDiscrimValMixtureDistr(int, 
const char*, const char*, Boolean, Boolean, Boolean, Boolean)’:
Validation/DiscriminateFunction/Comet/CometDiscrimValMixtureDistr.cxx:34:120: 
error: cannot call constructor 
‘CometDiscrimValMixtureDistr::CometDiscrimValMixtureDistr’ directly 
[-fpermissive]
Validation/DiscriminateFunction/Comet/CometDiscrimValMixtureDistr.cxx:34:120: 
error:   for a function-style cast, remove the redundant 
‘::CometDiscrimValMixtureDistr’ [-fpermissive]

I've been generally following this guide: 
http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3.

Any suggestions?

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