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Re: [GUSDEV] GUS install problem with Postgres and Mac OSX
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From: Nicolas J. <nic...@gm...> - 2012-03-23 09:04:22
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Hi again,
Thanks again for the help!
I just have one last question:
In the Install Guide for GUS, it is written that one should register the
GUS application framework with the following command:
$ ga +meta --commit
I'm not quite sure what this does, and when I do run it, I get the
following message:
Nicolas-work-iMac:bin Nicolas$ ga +meta --commit
ERROR: Database version does not match required version for Plugin.
Database Version: Plugin Version: 3.6
Is this registration something I should worry about? If so, any suggestions
as to what this problem might be?
Best regards,
Nicolas
On Fri, Mar 23, 2012 at 13:05, Mark Heiges <mh...@ug...> wrote:
> whew!
>
> On Mar 23, 2012, at 12:01 AM, Nicolas Joannin wrote:
>
> > Indeed, again, my mistake!
> > Thank you all for your help: BUILD SUCCESSFUL ;)
> >
> > Best regards,
> > Nicolas
> >
> >
> > On Fri, Mar 23, 2012 at 12:40, Mark Heiges <mh...@ug...> wrote:
> > Check the dbiDsn setting in your gus.config. What you sent earlier
> (dbiDsn=dbi:Pg:dbname=<my_db_name>) looks correct to me; make sure that
> hasn't changed. The error is symptomatic of missing the 'dbname=' prefix
> >
> >
> >
> >
> >
> > On Mar 22, 2012, at 11:20 PM, Nicolas Joannin wrote:
> >
> > > Hi Mark,
> > >
> > > Thanks: indeed, I made the mistake of adjusting the PATH with
> $GUS_HOME/bin etc. before actually exporting GUS_HOME.
> > >
> > > I've rerun the build GUS install -append and it now has a new error:
> > > perlGeneratedModel:
> > > [echo] generating Perl Objects
> > > [exec] GUS::ObjRelP::DbiDbHandle
> connect('varDB_2012','postgres',...) failed: missing "=" after "varDB_2012"
> in connection info string at
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 173
> > > [exec] Can't bless non-reference value at
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
> > >
> > > BUILD FAILED
> > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The following
> error occurred while executing this line:
> > > /Users/Nicolas/GUS/project_home/GUS/build.xml:258: exec returned: 255
> > >
> > > Thanks again for your help!
> > > Best regards,
> > > Nicolas
> > >
> > >
> > > Full output:
> > >
> > > Nicolas-work-iMac:bin Nicolas$ ./build GUS install -append
> > > 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
> > >
> > > defaultComponentInstall:
> > > [echo] .
> > > [echo] Installing GUS/ObjRelP
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > perlGeneratedModel:
> > > [echo] generating Perl Objects
> > > [exec] GUS::ObjRelP::DbiDbHandle
> connect('varDB_2012','postgres',...) failed: missing "=" after "varDB_2012"
> in connection info string at
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 173
> > > [exec] Can't bless non-reference value at
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
> > >
> > > 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: exec returned: 255
> > >
> > > Total time: 20 seconds
> > >
> > > On Fri, Mar 23, 2012 at 12:00, Mark Heiges <mh...@ug...> wrote:
> > > The includeantruntime warning is an ant 1.8 "feature". I'm pretty sure
> you can ignore that warning in this case, I don't see any abnormal
> repercussions from it, but we've not used that version of ant ourselves.
> You can google that warning for more information if you're curious.
> > >
> > > The generateGusObjects error makes me suspect that your PATH doesn't
> include $GUS_HOME/bin . You'll want something like
> > > export PATH=$GUS_HOME/bin:$PROJECT_HOME/install/bin:$PATH
> > >
> > > At this point the schema is installed in your database (log in with a
> client and confirm). So the next time run "build GUS install -append"
> (without the -installDBSchema) and it should resume with the "generating
> Perl Objects".
> > >
> > >
> > > On Mar 22, 2012, at 9:59 PM, Nicolas Joannin wrote:
> > >
> > > > 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
> > > > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
> >
>
>
>
|
