From: Nicolas J. <nic...@gm...> - 2012-03-23 01:59:58
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Hi Mark, I got the code from the subversion repository, but that was a couple weeks ago, I think. I've just tried with the latest svn update. I started all from scratch: I deleted the GUS folder I was working in and replaced it with the new. I run the install a first time and encountered the same ojdbc5.jar problem. So I added that file to the proper directory and rerun the install. This time I get different errors (see full output below): 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 [InstallSchema] ERROR [main] (InstallSchemaTask.java:122) - Null version, skipping. Note: You will need to manually add a version number to the DB 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:258: Execute failed: java.io.IOException: Cannot run program "generateGusObjects" (in directory "/Users/Nicolas/GUS/project_home/install"): error=2, No such file or directory The first one (with the "warning: 'includeantruntime'") occurs several times. Thanks for the quick responses! Best regards, Nicolas Here's the full output: 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 [InstallSchema] ERROR [main] (InstallSchemaTask.java:122) - Null version, skipping. Note: You will need to manually add a version number to the DB [InstallSchema] ERROR [main] (InstallSchemaTask.java:122) - Null version, skipping. Note: You will need to manually add a version number to the DB defaultComponentInstall: [echo] . [echo] Installing GUS/ObjRelP componentPartCopySub: [copy] Copying 3 files to /Users/Nicolas/GUS/gus_home/bin componentPartCopySub: [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP [copy] Copying 18 files to /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP componentPartCopySub: [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/doc/GUS/ObjRelP [copy] Copying 3 files to /Users/Nicolas/GUS/gus_home/doc/GUS/ObjRelP recordBuildState: [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/. build.info perlGeneratedModel: [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/Core [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/DoTS [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/RAD [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/SRes [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/TESS [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/PROT [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/Study [echo] generating Perl Objects 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:258: Execute failed: java.io.IOException: Cannot run program "generateGusObjects" (in directory "/Users/Nicolas/GUS/project_home/install"): error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:460) at java.lang.Runtime.exec(Runtime.java:593) at org.apache.tools.ant.taskdefs.Execute$Java13CommandLauncher.exec(Execute.java:862) at org.apache.tools.ant.taskdefs.Execute.launch(Execute.java:481) at org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:495) at org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:631) at org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:672) at org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:498) 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) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.<init>(UNIXProcess.java:53) at java.lang.ProcessImpl.start(ProcessImpl.java:91) at java.lang.ProcessBuilder.start(ProcessBuilder.java:453) ... 36 more Total time: 30 seconds On Fri, Mar 23, 2012 at 10:37, Mark Heiges <mh...@ug...> wrote: > Hi Nicolas, Are you using code from the gus subversion repository? If so, > do an svn update. This bug was fixed this morning. If not from subversion, > where did you get your code? > > -Mark > > On Mar 22, 2012, at 9:24 PM, Nicolas Joannin wrote: > > > 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 > > > > > > |