[Bioperl-l] Bptutorial.pl

[Paul Boutros]

Hi Peter,

> > c:\perl\bioperl-live> perl -c bptutorial.pl
> > Can't locate Bio/Tools/Run/Alignment/TCoffee.pm in @INC (@INC contains: .
> > C:/Perl/lib C:/Perl/site/lib) at bptutorial.pl line 3118.
> > BEGIN failed--compilation aborted at bptutorial.pl line 3118.
> 
> Thanks for finding this bug!  It should now be fixed in CVS.  Perhaps you
> can try it again (since I don't have a Windows machine and am not sure that
> my fix will work there)?

It does indeed work now.

> > I get the usual subroutine redefinition warnings as well as:
> >
> > Can't use string ("Bio::Tools::Run::StandAloneBlast") as a HASH ref
> > while "strict refs" in use at
> > C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm line 366.
> >
> > Based on the subroutine redefinitions, I would suggest that the running
> > instructions in bptutorial are changed from:
> > perl -w bptutorial.pl <parameters>
> > to just: perl bptutorial.pl <parameters>
> 
> This one is puzzling.  It should not be necessary (or IMO desirable) to turn
> off warnings when running the tutorial.  I am unable to reproduce the error
> on my Linux machine.  What version of StandAloneBlast.pm is the one in your
> directory C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm?

# $Id: StandAloneBlast.pm,v 1.26 2002/12/16 14:50:24 jason Exp $

Let me also point out that the subroutine redefinition warnings *will*
show up with the -w flag regardless.  (There was a recent thread about
this on the list)  So, for that reason alone it might be a good idea to
leave warnings off.  That would avoid scaring a newbie user with a screen
full of warnings the first time he/she tries to run the tutorial!

Paul