This is most likely a problem with your MySQL installation. We have had some reports with similar errors for some MySQL versions. It seems to be working well with 5.1.47 and 5.1.48 but not with 5.1.49. The latest version seems to be 5.1.52 but I don't know if anyone has tested it. Unfortunately, the 5.1 branch of MySQL has not been very stable so once you get something that works it is best to stick with it.
/Nicklas On 2010-11-05 22:22, Adam Halstead wrote: > After downloading the pre-compiled release of BASE2 (base-2.16.0.tar.gz) > I followed the installed instructions at: > http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.installation.html > > Failing at the BASE (database initialization) step. > I am running Ubuntu 10.10 64-bit running under Vmware. > Apache Tomcat/6.0.28 > > The output is below: > > ./initdb.sh root > [0%] --System information----------------------------- > BASE : 2.16.0 > Database : > jdbc:mysql://localhost/base2?characterEncoding=UTF-8&useCursorFetch=true&defaultFetchSize=100&useServerPrepStmts=true > Dialect : org.hibernate.dialect.MySQLInnoDBDialect > JDBC : com.mysql.jdbc.Driver; version 5.1 > Java : OpenJDK Runtime Environment; 1.6.0_20-b20; Sun Microsystems Inc. > OS : Linux; amd64; 2.6.35-22-generic > ------------------------------------------------- > [0%] Building database... > [0%] --create table `AnnotationSets` (`id` intege..................... > [0%] --create table `BioMaterialListMembers` (`bi..................... > [1%] --create table `DataFileTypes` (`id` integer..................... > [2%] --create table `GlobalDefaultSettings` (`id`..................... > [3%] --create table `Labels` (`id` integer not nu..................... > [4%] --create table `PluginConfigurations` (`id` ..................... > [5%] --create table `RawDataAgilent` (`id` intege..................... > [6%] --create table `Sessions` (`id` integer not ..................... > [7%] --create table `VirtualDbs` (`id` integer no..................... > [8%] --alter table `Annotations` add index FK2A17..................... > [9%] --alter table `ArrayDesigns` add index FK120..................... > [10%] --alter table `BioAssaySets` add index FKB8B..................... > [11%] --alter table `BioMaterialLists` add index F..................... > [12%] --alter table `BioWells` add index FK3CDF555..................... > [13%] --alter table `DataFileTypes` add index FK74..................... > [14%] --alter table `Experiments` add index FKC5BB..................... > [15%] --create index name_idx on `FileTypes` (`name`).................. > [16%] --alter table `GroupProjects` add index FK6E..................... > [17%] --alter table `Images` add index FK82BF6E98C..................... > [18%] --alter table `Jobs` add index FK2350763AAF7..................... > [19%] --alter table `PlateEventTypes` add index FK..................... > [20%] --alter table `PlateTypes` add index FKE9A8E..................... > [21%] --alter table `PluginConfigurations` add ind..................... > [22%] --alter table `PropertyFilters` add index FK..................... > [23%] --alter table `RawBioAssays` add index FKA9F..................... > [24%] --alter table `RawDataBZScan` add index FK2B..................... > [25%] --alter table `RawDataQuantArrayBiotin` add ..................... > [26%] --alter table `RoleKeys` add index FKF3F25BA..................... > [27%] --alter table `SpotImages` add index FK9774F..................... > [28%] --alter table `UserDefaultSettings` add inde..................... > [29%] --alter table `Wells` add index FK4F98945DCB... > [30%] Database built successfully. > [35%] Initialising database...15:32:35,546 ERROR Application:615 - > Exception when starting... > net.sf.basedb.core.BaseException: could not insert: > [net.sf.basedb.core.data.NewsData] > at net.sf.basedb.core.HibernateUtil.saveData(HibernateUtil.java:1162) > at > net.sf.basedb.core.HibernateUtil.testTransactions(HibernateUtil.java:1799) > at net.sf.basedb.core.Application.start(Application.java:512) > at net.sf.basedb.core.Install.initDatabase(Install.java:165) > at net.sf.basedb.install.InitDB.main(InitDB.java:74) > Caused by: org.hibernate.exception.GenericJDBCException: could not > insert: [net.sf.basedb.core.data.NewsData] > at > org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:140) > at > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:128) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66) > at > org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:64) > at > org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2329) > at > org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2836) > at > org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:71) > at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:267) > at > org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:321) > at > org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:204) > at > org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:130) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:210) > at > org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:56) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:195) > at > org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:50) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:93) > at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:705) > at org.hibernate.impl.SessionImpl.save(SessionImpl.java:693) > at org.hibernate.impl.SessionImpl.save(SessionImpl.java:689) > at net.sf.basedb.core.HibernateUtil.saveData(HibernateUtil.java:1153) > ... 4 more > Caused by: java.sql.SQLException: Incorrect arguments to mysqld_stmt_execute > at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1075) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3566) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3498) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1959) > at > com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1349) > at > com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:847) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2409) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2327) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2312) > at > com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105) > at > org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:94) > at > org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:57) > ... 20 more > > [70%] Database initialisation failed: could not insert: > [net.sf.basedb.core.data.NewsData] > > > net.sf.basedb.core.BaseException: could not insert: > [net.sf.basedb.core.data.NewsData] > at net.sf.basedb.core.Application.start(Application.java:618) > at net.sf.basedb.core.Install.initDatabase(Install.java:165) > at net.sf.basedb.install.InitDB.main(InitDB.java:74) > Caused by: net.sf.basedb.core.BaseException: could not insert: > [net.sf.basedb.core.data.NewsData] > at net.sf.basedb.core.HibernateUtil.saveData(HibernateUtil.java:1162) > at > net.sf.basedb.core.HibernateUtil.testTransactions(HibernateUtil.java:1799) > at net.sf.basedb.core.Application.start(Application.java:512) > ... 2 more > Caused by: org.hibernate.exception.GenericJDBCException: could not > insert: [net.sf.basedb.core.data.NewsData] > at > org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:140) > at > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:128) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66) > at > org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:64) > at > org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2329) > at > org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2836) > at > org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:71) > at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:267) > at > org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:321) > at > org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:204) > at > org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:130) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:210) > at > org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:56) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:195) > at > org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:50) > at > org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:93) > at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:705) > at org.hibernate.impl.SessionImpl.save(SessionImpl.java:693) > at org.hibernate.impl.SessionImpl.save(SessionImpl.java:689) > at net.sf.basedb.core.HibernateUtil.saveData(HibernateUtil.java:1153) > ... 4 more > Caused by: java.sql.SQLException: Incorrect arguments to mysqld_stmt_execute > at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1075) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3566) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3498) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1959) > at > com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1349) > at > com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:847) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2409) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2327) > at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2312) > at > com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105) > at > org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:94) > at > org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:57) > ... 20 more > > ------------------------------------------------------------------------------ > The Next 800 Companies to Lead America's Growth: New Video Whitepaper > David G. 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Listen Now! http://p.sf.net/sfu/SAP-dev2dev _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
