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[modeller_usage] 'import site' failed; use -v for traceback

when I execute Modeller 9v4 script I get python warning 
'import site' failed; use -v for traceback

Everything seems to work just fine though this message is a kind of
annoying. I`ve searched the list and tried to tweak PYTHONHOME/PATH vars
but that did not help. Furthermore I have python 2.5 installed and
modeller uses built-in 2.3. Considering that I have no intentions of
using external python modules could this message cause me a problem with
my work?
Thank you for your help.