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

John M.C. Ma manchunjohn-ma at uiowa.edu
Wed Jul 30 16:52:01 EDT 2008


Hi Chris and everyone, it goes on fine. Thanks for all the help! John

On Wed, Jul 30, 2008 at 2:28 PM, Chris Fields <cjfields at uiuc.edu> wrote:

> 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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