Thanks. I'll give it a try. Peter. Syed Haider wrote: > 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. >>
-- Peter Stevenson | [email protected] EMAP Computer Support | http://www.emouseatlas.org/emage MRC Human Genetics Unit | Phone: +44 (0)131 332 2471 Edinburgh EH4 2XU. U.K. | _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
