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

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