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Re: [GUSDEV] GUS install problem with Postgres and Mac OSX
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From: John I. <io...@gm...> - 2012-03-23 18:42:11
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Hi Nicolas,
I think this is related to the table core.DatabaseVersion, and that this
table should have a single row in it with "3.6" in the VERSION column. But
I don't know how that gets there.
Is this what you have? If that table is empty, my suggestion (unless
somebody else has a better one) is to insert a record with that value in
that column.
-- John
On Fri, Mar 23, 2012 at 5:03 AM, Nicolas Joannin
<nic...@gm...>wrote:
> 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
>> > > > > >
>> > > >
>> > > >
>> > > >
>> > >
>> > >
>> > >
>> >
>> >
>> >
>>
>>
>>
>
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