[Bioperl-l] Problems when trying to persist a sequence in my BioSQL database using, BioPerl

[Hilmar Lapp]

Hi Gabrielle,

(note that I have changed the mailing list to bioperl - whoever  
replies please cut biosql from the cc list, assuming that this indeed  
isn't BioSQL's fault)

given the error message below, Bio::SeqIO::genbank can be found, but  
it fails to load because it requires Bio::Species, which in turn  
imports support for weak references from Scalar::Util. The last step  
fails, causing loading Bio::Species to fail, which in turn causes  
Bio::SeqIO::genbank to fail to load.

The real question is why your version of Perl doesn't seem to have  
support for weak references (the reason for Scalar::Util failing to  
load). Could you give details on your OS version and your version of  
Perl (output of 'perl -V').

The question for BioPerl is whether there is a fall-back mechanism we  
might want to support if weak references aren't supported, rather than  
rendering the genbank parser unusable. Sendu or Chris - any thoughts  
on this?

	-hilmar

On Jun 24, 2008, at 10:49 AM, Gabrielle Doan wrote:

> Hi all,
>
> I am new to BioPerl and BioSQL so please excuse me if my question is  
> a bit simple. I followed the installation files in the current  
> version of BioPerl very strictly (I used the Bioperl 1.5.2,  
> Developer Release from the bioperl website). After successful  
> installation I tried to persist a genbank file in my BioSQL  
> database, which runs on a database server and is accessible using  
> the mysql command shell. When using bioperl I receive the following  
> error message:
>
> ================
>
> $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb -- 
> dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db- 
> data/ref_chr1.gbk
> Loading /local/doan/db-daten/ref_chr1.gbk ...
> Bio::SeqIO: genbank cannot be found
> Exception ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Failed to load module Bio::SeqIO::genbank. Weak references are  
> not implemented in the version of perl at /usr/lib/perl5/site_perl/ 
> 5.8.8/Bio/Species.pm line 91
> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ 
> Bio/Species.pm line 91.
> Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> SeqIO/genbank.pm line 172.
> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ 
> Bio/SeqIO/genbank.pm line 172.
> Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm line 425.
>
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/ 
> Bio/Root/Root.pm:427
> STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/ 
> 5.8.8/Bio/SeqIO.pm:555
> STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376
> STACK: /usr/bin/bp_load_seqdatabase.pl:541
> -----------------------------------------------------------
>
> For more information about the SeqIO system please see the SeqIO docs.
> This includes ways of checking for formats at compile time, not run  
> time
> Can't call method "next_seq" on an undefined value at /usr/bin/ 
> bp_load_seqdatabase.pl line 565.
>
> ================
>
> Unfortunately, even Google does not provide any hints when searching  
> for the particular message. It seems that for some reason the path  
> to the Bio::SeqIO::genbank module cannot be found. I am greateful  
> for any hint!
>
> Cheers,
> Gabrielle
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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