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

Sendu Bala bix at sendu.me.uk
Thu Jun 26 06:02:38 EDT 2008


Hilmar Lapp wrote:
> 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').

Given that it seems to be perl 5.8.8, I'm guessing this is the 
RedHat/Fedora issue:

http://search.cpan.org/~adamk/Task-Weaken-1.02/lib/Task/Weaken.pm


Solutions:
First try installing the latest version of Scalar::Util yourself:

perl -MCPAN -e shell
force install Scalar::Util

(and see that it gets installed in a place that is checked before the 
Fedora version, or overwrites the Fedora version)

If that doesn't work, you'll have to download and compile Perl yourself 
from source (don't use Fedora's installation system).


> 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?

Firstly, Task::Weaken should get added to Build.pl as a requirement, so 
people get better error messages. If we do that, however, the whole of 
BioPerl doesn't get installed, never mind just the genbank parser not 
being usable.

As for a fall-back mechanism, I'm not really sure how that would work. 
The easiest thing to do would be to just not deal with the species lines 
if Bio::Species doesn't work. Is that an acceptable fall-back? If not, 
more thought and discussion is needed. Make a proposal: what would you 
want to happen?


> 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


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