[Bioperl-l] Issue with HOWTO Beginners Examples from "Retrieving a sequence from a database" and beyond

[Fields, Christopher J]

Kevin,

This is no longer the latest release, but I don't think we have a newer PPM available yet (at least, I don't think we do).  The latest on CPAN is v1.6.901. This release updated the code to be compliant with perl 5.12 and up and fixed a few minor bugs, including the 'replacement list' one.  IIRC, ActivePerl and Strawberry Perl allow you to install from CPAN.

Also, the 'subroutine redefined' errors are generally Windows-specific and are from using the '-w' flag in the script shebang line.  Try removing that and see if things quiet down a bit.  Regardless, these are simply warnings, not errors.

chris

On Jun 7, 2012, at 2:56 PM, Kevin Farquhar wrote:

> Hi,
> 
> My Bioperl version is 1.6.1 and it runs on a Windows 7 64 bit Ultimate OS.
> I'm trying to receive a sequence from the genbank database, but am having
> no luck. What should I do?
> Attached to this email is the pl I'm using
> Here are the errors:
> 
> C:\Users\Kevin>perl C:\Perl64\lib\Perl\secondbioperl3.pl
> Name "main::seq_obj" used only once: possible typo at
> C:\Perl64\lib\Perl\secondb
> ioperl3.pl line 7.
> Replacement list is longer than search list at
> C:/Perl64/site/lib/Bio/Range.pm l
> ine 251.
> UNIVERSAL->import is deprecated and will be removed in a future perl at
> C:/Perl6
> 4/site/lib/Bio/Tree/TreeFunctionsI.pm line 94
> Subroutine new redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line
> 93, <
> GEN1> line 22.
> Subroutine start redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm
> line 115
> , <GEN1> line 22.
> Subroutine end redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line
> 144,
> <GEN1> line 22.
> Subroutine length redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm
> line 19
> 0, <GEN1> line 22.
> Subroutine location_type redefined at
> C:/Perl64/site/lib/Bio\Location\Simple.pm
> line 281, <GEN1> line 22.
> Subroutine to_FTstring redefined at
> C:/Perl64/site/lib/Bio\Location\Simple.pm li
> ne 328, <GEN1> line 22.
> Subroutine trunc redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm
> line 370
> , <GEN1> line 22.
> 
> C:\Users\Kevin>
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