[Bioperl-l] bptutorial.pl question, and appropriate bioperl version question

Sam Al-Droubi saldroubi at gmail.com
Sun Mar 26 19:12:49 EST 2006


Philip,

I am relatively new to bioperl and I started with 1.5.0 and then I upgraded
to 1.5.1 because of a bug.  I suggest you do the same.  As far as I know,
you don't need to uninstall the current version just install the new version
and I think everything will work fine.

On 3/26/06, Philip M Terry <pterry2 at unlnotes.unl.edu> wrote:
>
>
> Hello,
>
> Would anyone be able to help/comment on the following:
>
> version of bioperl: Distribution    B/BI/BIRNEY/bioperl-1.4.tar.gz
> (installed from CPAN)
> platform: Power Mac G5 OS X 10.4.5
> What trying to do: Practice/learn to run bptutorial.pl from
> ~/.cpan/build/bioperl-1.4, trying run_remoteblast
> Code that gives the error:
> philip-terrys-power-mac-g5:~/.cpan/build/bioperl-1.4 mterry$ perl -w
> bptutorial.pl 22
>
> Beginning run_remoteblast example...
> submitted Blast job
> retrieving results...      #line 3322 of bptutorial.pl
>
> -------------------- WARNING ---------------------
> MSG: Possible error (1) while parsing BLAST report!
> ---------------------------------------------------
> Use of uninitialized value in substitution (s///) at Bio/Tools/BPlite.pm
> line 337, <GEN3> line 30.
> Use of uninitialized value in substitution (s///) at Bio/Tools/BPlite.pm
> line 338, <GEN3> line 30.
> Use of uninitialized value in substitution (s///) at Bio/Tools/BPlite.pm
> line 339, <GEN3> line 30.
> Use of uninitialized value in pattern match (m//) at Bio/Tools/BPlite.pm
> line 341, <GEN3> line 30.
> philip-terrys-power-mac-g5:~/.cpan/build/bioperl-1.4 mterry$
>
> The variable $def never gets initialized at line 326 of BPlite.pm module.
>
> I note that Bio::Tools::BPlite module will not to be supported in future
> versions of bioperl.
>
> So should I go from bioperl ver 1.4 to ver 1.5.1 before proceeding to
> practice with bptutorial.pl?
>
> If so, do I need to delete/uninstall ver 1.4 first before installing ver
> 1.5.1?  If so, how should it be done?
>
> Thanks,
> Philip M. Terry, Ph.D.
> University of Nebraska-Lincoln
>
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>



--
Sincerely,
Sam Al-Droubi, M.S.



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