Re: [GUSDEV] GUS install problem with Postgres and Mac OSX

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Good morning Mark, Rodrigo and John,

Indeed, the ojdbc5.jar file helped to get further ahead :)
Unfortunately, there are still some errors (see below).

Best regards,
Nicolas

Nicolas-work-iMac:bin Nicolas$ ./build GUS install -append -installDBSchema
Buildfile: /Users/Nicolas/GUS/project_home/install/build.xml

install:
     [echo]  proj=GUS
     [echo]  comp=

defaultComponentInstall:
     [echo] .
     [echo] Installing CBIL/Bio

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing CBIL/CSP

defaultJavaCompile:
    [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing CBIL/Util

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing CBIL/Cider

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing CBIL/HQ

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing CBIL/TranscriptExpression

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing CBIL/ObjectMapper

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing GUS/Supported

defaultJavaCompile:
    [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing GUS/Community

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing GUS/DBAdmin

defaultJavaCompile:
    [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing GUS/GOPredict

defaultJavaCompile:
    [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing GusSchema/Definition

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

defaultComponentInstall:
     [echo] .
     [echo] Installing GUS/DBAdmin

defaultJavaCompile:
    [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds

recordBuildState:
[propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.
build.info

InstallSchema:
[InstallSchema]  INFO [main] (InstallSchemaTask.java:79) - Reading database
from
/Users/Nicolas/GUS/project_home/GusSchema/Definition/config/gus_schema.xml
[InstallSchema]  INFO [main] (SchemaReader.java:48) - Reading Database
[InstallSchema]  INFO [main] (Database.java:161) - Resolving Database
References
[InstallSchema]  INFO [main] (DatabaseValidator.java:57) - Validating
Database: 'null'
[InstallSchema]  INFO [main] (InstallSchemaTask.java:87) -  Overriding
individual tablespace specifications with value "GUS" from property file
[InstallSchema]  INFO [main] (DatabaseValidator.java:57) - Validating
Database: 'null'
[InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing Database
[InstallSchema]  INFO [main] (DatabaseValidator.java:57) - Validating
Database: 'null'
[InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing Database

BUILD FAILED
/Users/Nicolas/GUS/project_home/install/build.xml:38: The following error
occurred while executing this line:
/Users/Nicolas/GUS/project_home/GUS/build.xml:16: The following error
occurred while executing this line:
/Users/Nicolas/GUS/project_home/GusSchema/build.xml:63:
java.io.IOException: Error executing SQL: '

CREATE TABLE Core.AlgorithmInvocation (
 ALGORITHM_INVOCATION_ID NUMERIC(12,0)  NOT NULL,
 ALGORITHM_IMPLEMENTATION_ID NUMERIC(5,0)  NOT NULL,
 START_TIME TIMESTAMP NOT NULL,
 END_TIME TIMESTAMP NOT NULL,
 CPUS_USED NUMERIC(5,0) ,
 CPU_TIME FLOAT(126) ,
 RESULT VARCHAR(350)  NOT NULL,
 COMMENT_STRING VARCHAR(255) ,
 MODIFICATION_DATE TIMESTAMP NOT NULL,
 USER_READ NUMERIC(1,0)  NOT NULL,
 USER_WRITE NUMERIC(1,0)  NOT NULL,
 GROUP_READ NUMERIC(1,0)  NOT NULL,
 GROUP_WRITE NUMERIC(1,0)  NOT NULL,
 OTHER_READ NUMERIC(1,0)  NOT NULL,
 OTHER_WRITE NUMERIC(1,0)  NOT NULL,
 ROW_USER_ID NUMERIC(12,0)  NOT NULL,
 ROW_GROUP_ID NUMERIC(4,0)  NOT NULL,
 ROW_PROJECT_ID NUMERIC(4,0)  NOT NULL,
 ROW_ALG_INVOCATION_ID NUMERIC(12,0)  NOT NULL)' Error: ERROR: precision
for type float must be less than 54 bits
 at org.gusdb.dbadmin.util.JDBCStreamWriter.flush(JDBCStreamWriter.java:57)
at
org.gusdb.dbadmin.writer.RelationalDatabaseWriter.writeTable(RelationalDatabaseWriter.java:67)
 at
org.gusdb.dbadmin.writer.RelationalDatabaseWriter.writeTables(RelationalDatabaseWriter.java:43)
at
org.gusdb.dbadmin.writer.PostgresWriter.writeDatabase(PostgresWriter.java:68)
 at org.gusdb.dbadmin.writer.SchemaWriter.write(SchemaWriter.java:34)
at
org.gusdb.dbadmin.util.InstallSchemaTask.execute(InstallSchemaTask.java:99)
 at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
 at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
 at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
 at org.apache.tools.ant.Target.execute(Target.java:392)
at org.apache.tools.ant.Target.performTasks(Target.java:413)
 at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
 at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
 at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
 at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
 at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
 at org.apache.tools.ant.Target.execute(Target.java:392)
at org.apache.tools.ant.Target.performTasks(Target.java:413)
 at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
 at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
 at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
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:597)
at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
 at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:392)
 at org.apache.tools.ant.Target.performTasks(Target.java:413)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
 at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
 at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
at org.apache.tools.ant.Main.runBuild(Main.java:811)
 at org.apache.tools.ant.Main.startAnt(Main.java:217)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
 at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

Total time: 20 seconds

On Thu, Mar 22, 2012 at 23:23, Mark Heiges <mh...@ug...> wrote:

> I have confirmed that the ojdbc jar is required for the code to compile.
>
> -Mark
>
> On Mar 22, 2012, at 10:09 AM, John Iodice wrote:
>
> > Hi Nicolas,
> >
> > That dbVendor setting looks right; I think that your configuration is
> correct for a Postgres install (and that I was mistaken to think that the
> install is looking for oracle.jdbc.OracleDriver because it's configured to
> use Oracle).
> >
> > Looking in my own $GUS_HOME/lib/java/db_driver directory, I see that I
> have both Oracle and Postgres drivers, though I only use Oracle. Maybe both
> are required to compile the Java? These are the files I have there:
> >
> > $ ls $GUS_HOME/lib/java/db_driver/
> > ojdbc5.jar  postgresql-8.3-603.jdbc3.jar
> >
> > I see that ojdbc5.jar does contain oracle/jdbc/OracleDriver.class. I
> suggest you try downloading that jarfile. You can get it from here:
> http://www.oracle.com/technetwork/database/enterprise-edition/jdbc-111060-084321.html
> >
> > -- John
> >
>