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bioperl help?

by usless_blonde (Initiate)
on Oct 08, 2003 at 13:18 UTC ( [id://297568]=perlquestion: print w/replies, xml ) Need Help??

usless_blonde has asked for the wisdom of the Perl Monks concerning the following question:

hello!
Any bioperl experts? The code is simlar to the synopsis but i keep getting the error.
Can't call method "algorithm" without a package or object reference at /usr/lib/ perl5/site_perl/5.8.0/Bio/SearchIO/Writer/TextResultWriter.pm line 197.
what on earth does that mean??

Replies are listed 'Best First'.
Re: bioperl help?
by Abigail-II (Bishop) on Oct 08, 2003 at 13:48 UTC
    Most likely it means that on line 197 of the file /usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/Writer/TextResultWriter.pm, it is attempted to call the method 'algorithm' on something that isn't a package or object references. Usually it means you have something like:
    $obj -> algorithm ();
    where $obj is undefined, or an otherwise plain scalar. Now, I expect you aren't working on TextResultWriter.pm, but on some file that calls (directly, or indirectly) a function in TextResultWriter.pm that contains this line. Then it's very well possible you aren't passing the appropriate arguments. Check your arguments. Make sure you pass objects where the function expects objects.

    But of course, this is mostly guessing. You aren't showing any code.

    Abigail

Re: bioperl help?
by sunadmn (Curate) on Oct 08, 2003 at 13:44 UTC
    This sounds like either the PM is not installed or that it was not installed correctly.
    Just go to search.cpan.org and search for the pm (TextResultWriter.pm) which shows to live inside this PerlMod Bio::SearchIO::Writer::TextResultWriter.

    -Sunadmn
Re: bioperl help?
by Anonymous Monk on Oct 08, 2003 at 13:39 UTC

    I recognize that error, but can't put my finger on it. Can you show the specific code?

      I recognize that error, but can't put my finger on it.
      Put your finger on `perldoc perldiag'   :)
      Can't call method ``%s'' without a package or object reference
      (F) You used the syntax of a method call, but the slot filled by the object reference or package name contains an expression that returns a defined value which is neither an object reference nor a package name. Something like this will reproduce the error:
          $BADREF = 42;
          process $BADREF 1,2,3;
          $BADREF->process(1,2,3);

      MJD says "you can't just make shit up and expect the computer to know what you mean, retardo!"
      I run a Win32 PPM repository for perl 5.6.x and 5.8.x -- I take requests (README).
      ** The third rule of perl club is a statement of fact: pod is sexy.

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