Very sorry about the confusion. I had a little bit of a versioning problem. I modified the error message line after I pasted in the code for the script to get a more informative error message, and forgot to fix the code. The modified line looks like this: 
copy($localfile, $installfile)
   or die "$localfile unable to copy to $installfile : $!\n";

[download]

That said, demerphq helped me track down the problem. The problematic files where read-only, and apparently File::Copy won't let you copy over read-only files (even if you are the Administrator). I modified the code to add lines like this: 

fixreadonly($plugindir) if $^O =~ /win32/i;

sub fixreadonly {
  my $dir = shift;
  my $unsetreadonly = Bio::Root::IO->catfile( $dir, "*.*");
  system("attrib -r /s $unsetreadonly");
}

[download]

Scott
Project coordinator of the Generic Model Organism Database Project

In reply to Re: Re: File::Copy dying on Win2k when target file already there by scain
in thread File::Copy dying on Win2k when target file already there by scain

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