update packages from local

Thanks. But I after I restarted R, it is still the old version of  
the package that is
loaded. Am I using the update.packages() correctly?

Apparently not.

I'm not an expert at this so it's perfectly possible that someone  
smarter could look at your first email and tell you what went wrong,  
although it seemed lacking in several details.  If I were you, I would  
be checking to see what my .libPaths value was, perhaps using a  
destdir argument and not trusting the value of working directory to  
determine where the source was coming from, but instead specifying  
absolute paths. You might consider an "oldPkgs" argument.

(You might consider including the results of sessionInfo() and the  
beginning and ending of the compilation output, and I would also not  
be trimming the email chain.)

Regards,
Wayne (Yanwei) Zhang

David Winsemius, MD
Heritage Laboratories
West Hartford, CT