[BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb

[Hilmar Lapp]

Hi Nick,

this is working fine for me, using perl v5.8.8. You may have noticed  
that DBI does have a method 'connect'.

Your perl reports to be 5.10, and to have been built for Mac OSX, yet  
it is a binary from ActiveState. Is my interpretation correct that you  
installed this on top of or in place of Mac OSX's native perl v5.8.8?  
Correspondingly, are you sure that 'perl' (which is what you are  
calling below), /usr/bin/perl (which is what the script executes), and  
cpan all are the same perl?

If this is all correct and all the right platform, could you try and  
edit the following code (starting at line 323):

my $dbh = DBI->connect($dsn,
		       $user,
		       $pass,
		       { RaiseError => 0,
			 AutoCommit => 1,
			 PrintError => 0,
		       }
		      ) or die $DBI::errstr;

by removing the 'or die $DBI::errstr' part. This would be hoping that  
it's an incompatibility for v5.10.

BTW are you sure you need perl 5.10? You will encounter various perl  
software that has not been tested against it yet (though I think  
Bioperl has been fixed meanwhile to be compatible).

	-hilmar

On Sep 2, 2008, at 7:52 PM, Nick Matzke wrote:

> Hi all,
>
> (sorry that I cross-posted this to the biopython lis, I only just  
> realized I should get on the bioSQL list)
>
>
>
> I'm following the BioSQL tutorial at the biopython website (http://www.biopython.org/wiki/BioSQL#NCBI_Taxonomy 
>  ).  I can get bioseqdb to work, and the biosql python scripts etc.
>
> However I can't get these directions to work in loading the taxonomy  
> database into bioseqdb.  I get: "Can't locate object method  
> "connect" via package "DBI" "
>
> I double-checked to make sure I've got DBI in perl (see error  
> message below) but that doesn't seem to help.
>
> Any help appreciated!
> Nick
>
>
>
> commands/returns:
> ===========================
> mws2:/bioinformatics/eg nick$ perl -v
>
> This is perl, v5.10.0 built for darwin-thread-multi-2level
> (with 3 registered patches, see perl -V for more detail)
>
> Copyright 1987-2007, Larry Wall
>
> Binary build 1002 [283697] provided by ActiveState http://www.ActiveState.com
> Built Jan 10 2008 11:08:33
>
> Perl may be copied only under the terms of either the Artistic  
> License or the
> GNU General Public License, which may be found in the Perl 5 source  
> kit.
>
> Complete documentation for Perl, including FAQ lists, should be  
> found on
> this system using "man perl" or "perldoc perl".  If you have access  
> to the
> Internet, point your browser at http://www.perl.org/, the Perl Home  
> Page.
>
>
>
>
>
>
> mws2:/bioinformatics/eg nick$ sudo cpan DBI
> Password:
>
> CPAN: Storable loaded ok (v2.18)
> Going to read /usr/local/Metadata
>  Database was generated on Wed, 23 Jul 2008 10:02:50 GMT
> CPAN: LWP::UserAgent loaded ok (v5.810)
> CPAN: Time::HiRes loaded ok (v1.9711)
> Fetching with LWP:
>  http://ppm.activestate.com/CPAN/authors/01mailrc.txt.gz
> CPAN: YAML loaded ok (v0.66)
> Going to read /Users/nick/.cpan/sources/authors/01mailrc.txt.gz
> ............................................................................DONE
> Fetching with LWP:
>  http://ppm.activestate.com/CPAN/modules/02packages.details.txt.gz
> Going to read /Users/nick/.cpan/sources/modules/ 
> 02packages.details.txt.gz
>  Database was generated on Mon, 01 Sep 2008 10:02:51 GMT
> ............................................................................DONE
> Fetching with LWP:
>  http://ppm.activestate.com/CPAN/modules/03modlist.data.gz
> Going to read /Users/nick/.cpan/sources/modules/03modlist.data.gz
> ............................................................................DONE
> Going to write /usr/local/Metadata
> DBI is up to date (1.607).
>
>
>
>
>
>
> mws2:/bioinformatics/eg nick$ /bioinformatics/pythonstuff/ 
> biosql-1.0.0/scripts/load_ncbi_taxonomy.pl --dbname bioseqdb -- 
> driver mysql --dbuser root --download true
>
>
> Can't locate object method "connect" via package "DBI" at / 
> bioinformatics/pythonstuff/biosql-1.0.0/scripts/ 
> load_ncbi_taxonomy.pl line 323.
>
> mws2:/bioinformatics/eg nick$
> ===========================
>
>
>
> Additional sleuthing:
> ===========================
> Based on some web advice on this general error I also did this:
>
> sudo cpan DBD::mysql
>
> ...which did install something that wasn't installed.  But the same  
> error resulted when the load_ncbi_taxonomy.pl script was run.
> ===========================
>
>
> Perl *does* successfully recognize DBI and DBD::mysql, so e.g. not  
> finding them in @INC or something doesn't seem to be the problem...
>
> (these commands return '1' if the module is successfully found)
> ============
> perl -MDBD::mysql -e 'print 1'
> 1
>
> perl -MDBI -e 'print 1'
> 1
> ============
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> 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 :
===========================================================