Hi Peter,
there is a .cnf (my.cnf) file associated with the mysql db server that
contains the configuration for db server. please set the following
variable if not set already or set to 16M:
max_allowed_packet = 32M
once done, kill and restart the db server and see if that helps,
you can also set it from shell as :
mysqld --max_allowed_packet = 32M
Best,
Syed
On 08/03/2011 15:45, Peter Stevenson wrote:
Hi Syed,
Yes, I should have said, it is my own database - EMAGE Biomart.
Peter.
Syed Haider wrote:
Hi Peter,
is the database in discussion your own ? i mean are you managing db
server yourself ?
Thanks
Syed
On 08/03/2011 15:27, Peter Stevenson wrote:
I'm using v0.7 and sometimes getting errors similar to the example in
the stack trace below.
I have only noticed it in linked dataset queries.
For this particular query, results are returned OK for 10 rows, or 20
rows but asking for 50 rows of
results sets off the exception.
It seems to be data dependent, so that the same set of filters and
attributes with different input
values will run without error.
Any thoughts on why this might be happening?
Stack trace below:-
Serious Error: Error during query execution: Got a packet bigger than
'max_allowed_packet' bytes
ERROR: caught BioMart::Exception::Database: Error during query
execution: Got a packet bigger than
'max_allowed_packet' bytes
If you repeatedly get directed to this error page, there may be a
problem with your current session
parameters. To clear your session and start with a clean slate, please
click the New button below.
Stacktrace:
Exception::Class::Base::throw
/export/system0/biomart/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241
BioMart::Dataset::TableSet::_fillAttributeTableWith
/export/system0/biomart/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124
BioMart::Dataset::TableSet::_getResultTable
/export/system0/biomart/biomart-perl/lib/BioMart/DatasetI.pm:1170
BioMart::DatasetI::getResultTable
/export/system0/biomart/biomart-perl/lib/BioMart/ResultTable.pm:195
BioMart::ResultTable::_getBatch
/export/system0/biomart/biomart-perl/lib/BioMart/ResultTable.pm:247
BioMart::ResultTable::hasMoreRows
/export/system0/biomart/biomart-perl/lib/BioMart/ResultTable.pm:248
BioMart::ResultTable::hasMoreRows
/export/system0/biomart/biomart-perl/lib/BioMart/AttributeTable.pm:169
BioMart::AttributeTable::nextRow
/export/system0/biomart/biomart-perl/lib/BioMart/ResultTable.pm:256
BioMart::ResultTable::nextRow
/export/system0/biomart/biomart-perl/lib/BioMart/Formatter/HTML.pm:103
BioMart::Formatter::HTML::nextRow
/export/system0/biomart/biomart-perl/lib/BioMart/QueryRunner.pm:259
BioMart::QueryRunner::printResults
/export/system0/biomart/biomart-perl/lib/BioMart/Web.pm:2439
(eval) /export/system0/biomart/biomart-perl/lib/BioMart/Web.pm:2198
BioMart::Web::handle_request
/export/system0/biomart/biomart-perl/cgi-bin/martview:100
(eval) /export/system0/biomart/biomart-perl/cgi-bin/martview:99
ModPerl::ROOT::ModPerl::Registry::export_system0_biomart_biomart_2dperl_cgi_2dbin_martview::handler
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
(eval)
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0
Regards,
Peter.
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