Error on post-processing

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Error on post-processing

Paulo Nuin
Hi

I got an error while building WormMine on the transfer-sequence step of post-processing (unfortunately I don’t have the output of the pbuild command). I tried running the post-processing task from the integrate directory and got this error (for any action):


BUILD FAILED                                                                                                                                                          
/mnt/data/intermine_dev/imbuild/integrate.xml:54: no source set, try "ant -Dsource=all" or "ant -Dsource=source1,source2"                                            
        at org.intermine.task.Integrate.execute(Integrate.java:82)                                                                                                    
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)                                                                                        
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)                                                                                              
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)                                                                      
        at java.lang.reflect.Method.invoke(Method.java:606)                                                                                                            
        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)


I have found another thread with a similar error and tried a couple of things from there, to no success.

Any help appreciated.

Thanks
Paulo
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Re: Error on post-processing

joe carlson


On 06/13/2016 01:23 PM, Paulo Nuin wrote:
> Hi
>
> I got an error while building WormMine on the transfer-sequence step of post-processing (unfortunately I don’t have the output of the pbuild command). I tried running the post-processing task from the integrate directory and got this error (for any action):

I'm not one of the intermine folks, but this one looks easy enough to
answer.

You should be in the postprocess/ directory, not the integrate/
directory. And the syntax of the ant command is slightly different. Use

ant -Daction=transfer-sequences

(as opposed to "ant -Dsource=...") And be sure that <post-process
name="transfer-sequences" /> is in your project.xml. Alternatively, you
can just type 'ant' in the postprocess directory and all tasks will be done.

Joe

>
> BUILD FAILED
> /mnt/data/intermine_dev/imbuild/integrate.xml:54: no source set, try "ant -Dsource=all" or "ant -Dsource=source1,source2"
>          at org.intermine.task.Integrate.execute(Integrate.java:82)
>          at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>          at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>          at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>          at java.lang.reflect.Method.invoke(Method.java:606)
>          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)
>
>
> I have found another thread with a similar error and tried a couple of things from there, to no success.
>
> Any help appreciated.
>
> Thanks
> Paulo
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: Error on post-processing

Paulo Nuin
Hi Joe

Yes, I used -Daction, but from the integrate. I will try from the postprocess.

Thanks a lot

Paulo


On Jun 13, 2016, at 2:28 PM, Joe Carlson <[hidden email]> wrote:



On 06/13/2016 01:23 PM, Paulo Nuin wrote:
Hi

I got an error while building WormMine on the transfer-sequence step of post-processing (unfortunately I don’t have the output of the pbuild command). I tried running the post-processing task from the integrate directory and got this error (for any action):

I'm not one of the intermine folks, but this one looks easy enough to answer.

You should be in the postprocess/ directory, not the integrate/ directory. And the syntax of the ant command is slightly different. Use

ant -Daction=transfer-sequences

(as opposed to "ant -Dsource=...") And be sure that <post-process name="transfer-sequences" /> is in your project.xml. Alternatively, you can just type 'ant' in the postprocess directory and all tasks will be done.

Joe


BUILD FAILED
/mnt/data/intermine_dev/imbuild/integrate.xml:54: no source set, try "ant -Dsource=all" or "ant -Dsource=source1,source2"
        at org.intermine.task.Integrate.execute(Integrate.java:82)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        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)


I have found another thread with a similar error and tried a couple of things from there, to no success.

Any help appreciated.

Thanks
Paulo
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
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