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Hibernate version:
Hibernate 3.0.5
Mapping documents:
<hibernate-mapping>
<class name="A" table="a" >
<id name="id" unsaved-value="null">
<generator class="assigned"/>
</id>
<many-to-one
name="b" class="B" not-null="true" unique="true" />
...

<hibernate-mapping>
<class name="B" table="b" >
<id name="bb" unsaved-value="null">
<column name="bb" length="12" sql-type="char(12)" not-null="true"/>
<generator class="assigned"/>
</id>
...

Code between sessionFactory.openSession() and session.close():
Configuration cc = new Configuration();
cc.configure();
new SchemaExport(cc).create(false, true);
Full stack trace of any exception that occurs:
2005-10-11 13:49:43,906 ERROR SchemaExport:167 - Unsuccessful: alter table a add constraint FK17E3CD0A98C01 foreign key (b) references b
2005-10-11 13:49:43,906 ERROR SchemaExport:168 - Column 'b.bb' is not the same data type as referencing column 'a.b' in foreign key 'FK17E3CD0A98C01'.

Name and version of the database you are using:
ms sql 2000 sp4
The generated SQL (show_sql=true):

Debug level Hibernate log excerpt:
2005-10-11 13:18:58,875 DEBUG SchemaExport:161 - alter table a
add constraint FK17E3CD0A98C01
foreign key (b)
references b
2005-10-11 13:18:58,921 DEBUG NewPooledConnection:304 - com.mchange.v2.c3p0.impl.NewPooledConnection@1551b0 handling a throwable.
java.sql.SQLException: Column 'b.bb' is not the same data type as referencing column 'a.b' in foreign key 'FK17E3CD0A98C01'.
at net.sourceforge.jtds.jdbc.SQLDiagnostic.addDiagnostic(SQLDiagnostic.java:364)
at net.sourceforge.jtds.jdbc.TdsCore.tdsErrorToken(TdsCore.java:2754)
at net.sourceforge.jtds.jdbc.TdsCore.nextToken(TdsCore.java:2195)
at net.sourceforge.jtds.jdbc.TdsCore.getMoreResults(TdsCore.java:620)
at net.sourceforge.jtds.jdbc.JtdsStatement.processResults(JtdsStatement.java:483)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeSQL(JtdsStatement.java:445)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeImpl(JtdsStatement.java:623)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeUpdate(JtdsStatement.java:1042)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeUpdate(JtdsStatement.java:999)
at com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64)
at org.hibernate.tool.hbm2ddl.SchemaExport.execute(SchemaExport.java:163)
at org.hibernate.tool.hbm2ddl.SchemaExport.create(SchemaExport.java:99)
at AppMain.databaseSchemaOlustur(AppMain.java:117)
at AppMain.main(AppMain.java:46)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:86)
2005-10-11 13:18:58,921 DEBUG SqlUtils:83 - Attempted to convert SQLException to SQLException. Leaving it alone. [SQLState: S1000; errorCode: 1778]
java.sql.SQLException: Column 'b.bb' is not the same data type as referencing column 'a.b' in foreign key 'FK17E3CD0A98C01'.
at net.sourceforge.jtds.jdbc.SQLDiagnostic.addDiagnostic(SQLDiagnostic.java:364)
at net.sourceforge.jtds.jdbc.TdsCore.tdsErrorToken(TdsCore.java:2754)
at net.sourceforge.jtds.jdbc.TdsCore.nextToken(TdsCore.java:2195)
at net.sourceforge.jtds.jdbc.TdsCore.getMoreResults(TdsCore.java:620)
at net.sourceforge.jtds.jdbc.JtdsStatement.processResults(JtdsStatement.java:483)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeSQL(JtdsStatement.java:445)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeImpl(JtdsStatement.java:623)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeUpdate(JtdsStatement.java:1042)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeUpdate(JtdsStatement.java:999)
at com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64)
at org.hibernate.tool.hbm2ddl.SchemaExport.execute(SchemaExport.java:163)
at org.hibernate.tool.hbm2ddl.SchemaExport.create(SchemaExport.java:99)
at AppMain.databaseSchemaOlustur(AppMain.java:117)
at AppMain.main(AppMain.java:46)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:86)
2005-10-11 13:18:58,921 DEBUG SqlUtils:87 - Nested SQLException or SQLWarning:
java.sql.SQLException: Could not create constraint. See previous errors.
at net.sourceforge.jtds.jdbc.SQLDiagnostic.addDiagnostic(SQLDiagnostic.java:364)
at net.sourceforge.jtds.jdbc.TdsCore.tdsErrorToken(TdsCore.java:2754)
at net.sourceforge.jtds.jdbc.TdsCore.nextToken(TdsCore.java:2195)
at net.sourceforge.jtds.jdbc.TdsCore.getMoreResults(TdsCore.java:625)
at net.sourceforge.jtds.jdbc.JtdsStatement.processResults(JtdsStatement.java:483)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeSQL(JtdsStatement.java:445)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeImpl(JtdsStatement.java:623)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeUpdate(JtdsStatement.java:1042)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeUpdate(JtdsStatement.java:999)
at com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64)
at org.hibernate.tool.hbm2ddl.SchemaExport.execute(SchemaExport.java:163)
at org.hibernate.tool.hbm2ddl.SchemaExport.create(SchemaExport.java:99)
at AppMain.databaseSchemaOlustur(AppMain.java:117)
at AppMain.main(AppMain.java:46)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:86)
2005-10-11 13:18:58,921 DEBUG DefaultConnectionTester:67 - Testing a Connection in response to an Exception:
java.sql.SQLException: Column 'b.bb' is not the same data type as referencing column 'a.b' in foreign key 'FK17E3CD0A98C01'.
at net.sourceforge.jtds.jdbc.SQLDiagnostic.addDiagnostic(SQLDiagnostic.java:364)
at net.sourceforge.jtds.jdbc.TdsCore.tdsErrorToken(TdsCore.java:2754)
at net.sourceforge.jtds.jdbc.TdsCore.nextToken(TdsCore.java:2195)
at net.sourceforge.jtds.jdbc.TdsCore.getMoreResults(TdsCore.java:620)
at net.sourceforge.jtds.jdbc.JtdsStatement.processResults(JtdsStatement.java:483)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeSQL(JtdsStatement.java:445)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeImpl(JtdsStatement.java:623)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeUpdate(JtdsStatement.java:1042)
at net.sourceforge.jtds.jdbc.JtdsStatement.executeUpdate(JtdsStatement.java:999)
at com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64)
at org.hibernate.tool.hbm2ddl.SchemaExport.execute(SchemaExport.java:163)
at org.hibernate.tool.hbm2ddl.SchemaExport.create(SchemaExport.java:99)
at AppMain.databaseSchemaOlustur(AppMain.java:117)
at AppMain.main(AppMain.java:46)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:86)
2005-10-11 13:18:58,921 ERROR SchemaExport:167 - Unsuccessful: alter table aadd constraint FK17E3CD0A98C01 foreign key (b) references b
2005-10-11 13:18:58,937 ERROR SchemaExport:168 - Column 'b.bb' is not the same data type as referencing column 'a.b' in foreign key 'FK17E3CD0A98C01'.

Half solution:
if I change char(12) to varchar(12) then it is ok.
<hibernate-mapping>
<class name="B" table="b" >
<id name="bb" unsaved-value="null">
<column name="bb" length="12" sql-type="varchar(12)" not-null="true"/>
<generator class="assigned"/>
</id>
...

why I can't use char(12)?

Use following column mapping:

You should not specify "(12)" in sql-type attribute because there is no such SQL type "char(12)". You set the length of column in the length attribute.[/b]