[Bioperl-l] Issues on Bio::Tools::Primer3->next_primer

Jason Stajich jason at bioperl.org
Wed Jul 30 14:40:39 EDT 2008


yeah I don't know that the patch went in correctly, not sure if it  
was applied against the same version?
Roy can you double check how this should look.

-jason
On Jul 30, 2008, at 11:33 AM, John M.C. Ma wrote:

> Hi Roy,
>
> I have checked out this from svn. However, there was a compile-time  
> error
> for primer3.pm:
>
> syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line  
> 380,
> near "elsif"
> Global symbol "%args" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382.
> Global symbol "$key" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382.
> Global symbol "$self" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382.
> Can't use global $1 in "my" at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 389, near "=$1"
> Global symbol "$maxlocation" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390.
> Global symbol "$maxlocation" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390.
> Global symbol "$location" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 393.
> Global symbol "$location" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394.
> Global symbol "$maxlocation" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394.
> Global symbol "$maxlocation" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394.
> Global symbol "$location" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394.
> Global symbol "$location" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 396.
> Global symbol "%results" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399.
> Global symbol "$location" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399.
> Global symbol "$self" requires explicit package name at
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399.
> syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line  
> 400,
> near "}"
> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm has too many errors.
> Compilation failed in require at
> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145.
> BEGIN failed--compilation aborted at
> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145.
> Compilation failed in require at
> /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9.
> BEGIN failed--compilation aborted at
> /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9.
>
> Best regards,
>
> John
>
> On Wed, Jul 30, 2008 at 12:16 PM, Roy Chaudhuri  
> <roy.chaudhuri at gmail.com>wrote:
>
>> This is now fixed in bioperl-live thanks to Roy's patch (which  
>> seemed to
>>> post to bugzilla just fine).
>>>
>>
>> Thanks for adding in the patch. The bugzilla problems were an  
>> issue with
>> cookies using Firefox, it worked when I resorted to Internet  
>> Explorer.
>>
>> John- I should have mentioned in my previous post, if you have any  
>> problems
>> installing the patch (or upgrading from bioperl-live) then creating a
>> Bio::Seq object from your raw sequence and supplying that to the -seq
>> argument of new() is a suitable workaround.
>>
>>
>> Roy.
>> --
>> Dr. Roy Chaudhuri
>> Department of Veterinary Medicine
>> University of Cambridge, U.K.
>>
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