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Use of uninitialized value in length at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1064. #101

Open cjfields opened 8 years ago

cjfields commented 8 years ago

Author Name: Dan Bolser (Dan Bolser) Original Redmine Issue: 3206, https://redmine.open-bio.org/issues/3206 Original Date: 2011-04-15 Original Assignee: Bioperl Guts

I’m loading a simple GFF3 file (attached) that validates correctly here [1] using the following command:

 bp_seqfeature_load.pl --create --dsn my_database:mysql.host.here.ac.uk --user me --pass secret gene_test.gff

It seems to load fine, and there are no apparent errors. I’ve attached a dump of the database.

When I run a simple BioPerl script against the database [2], I see the following error:

Use of uninitialized value in length at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1064.

I tried to debug this by creating a test script [3], but I don’t see any errors. This could be because my test script is not testing in the same way.

Let me know what other info you need.

Dan.

[1] http://modencode.oicr.on.ca/cgi-bin/validate\_gff3\_online [2] https://gist.github.com/921515 [3] https://gist.github.com/921519

cjfields commented 8 years ago

Original Redmine Comment Author Name: Dan Bolser Original Date: 2011-04-18T09:32:47Z

Here is a link to the mailing list thread on the topic of this issue:

cjfields commented 8 years ago

Original Redmine Comment Author Name: Dan Bolser Original Date: 2011-05-03T11:23:50Z

Not sure if this is related, but I’m now seeing errors like this when calling ‘features’ on a SeqFeature::Store database:

Use of uninitialized value in length at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1064, <> line 1968.

cjfields commented 8 years ago

Original Redmine Comment Author Name: Dan Bolser Original Date: 2011-05-03T17:55:25Z

Dan Bolser wrote:

Not sure if this is related, but I’m now seeing errors like this when calling ‘features’ on a SeqFeature::Store database:

Use of uninitialized value in length at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1064, <> line 1968.

Please ignore me.