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

Chris Fields cjfields at uiuc.edu
Wed Jul 30 15:28:31 EDT 2008


Okay, patched the correct one (Bio::Tools::Run::Primer3); I previously  
patched Bio::Tools::Primer3 (and the patch succeeded!).  Ran tests and  
everything passes.  John can you try this one out to see if that fixes  
everything?

chris

On Jul 30, 2008, at 1:40 PM, Jason Stajich wrote:

> 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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>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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