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

John M.C. Ma manchunjohn-ma at uiowa.edu
Wed Jul 30 14:33:09 EDT 2008


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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