[BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb
Nick Matzke
matzke at berkeley.edu
Wed Sep 3 03:57:02 UTC 2008
Hi Hilmar!
Thanks, that's a good thought. But I just tried running it on the
default 5.8.6 (I have MacOX 10.4), same result:
==========================================
mws2:~ nick$ perl5.8.6 -MDBD::mysql -e 'print 1'
1
mws2:~ nick$ perl5.8.6 -MDBI -e 'print 1'
1
mws2:~ nick$ perl5.8.6 -v
This is perl, v5.8.6 built for darwin-thread-multi-2level
(with 4 registered patches, see perl -V for more detail)
Copyright 1987-2004, Larry Wall
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:~ nick$ perl5.8.6
/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.
==========================================
Just for kicks, I thought it might be a permission issue, so I tried it
with sudo also, at least I got a different error:
==================
mws2:~ nick$ sudo perl5.8.6
/bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl
--dbname bioseqdb --driver mysql --dbuser root --download true
Password:
Can't locate DBI.pm in @INC (@INC contains:
/System/Library/Perl/5.8.6/darwin-thread-multi-2level
/System/Library/Perl/5.8.6
/Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6
/Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level
/Network/Library/Perl/5.8.6 /Network/Library/Perl
/System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at
/bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl
line 195.
BEGIN failed--compilation aborted at
/bioinformatics/pythonstuff/biosql-1.0.0/scripts/load_ncbi_taxonomy.pl
line 195.
=====================
(As for why I installed ActivePerl -- I don't remember, but it seemed
like a good idea at the time when I was installing various packages and
something or other requested or suggested the newer version. I was a
total noob at the time. Still am, sorta...)
Nick
Hilmar Lapp wrote:
> 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
>
--
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page:
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu
Office hours for Bio1B, Spring 2008: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)
Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================
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