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Package 142/479HostnameOS / ArchBUILDCHECKBUILD BIN
ENVISIONQuery 1.1.2
Alex Lisovich , Roger Day
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ENVISIONQuery
Last Changed Rev: 54973 / Revision: 56603
Last Changed Date: 2011-04-19 19:42:31 -0700 (Tue, 19 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  ERROR  skipped 
liverpool Windows Server 2003 R2 (32-bit) / x64 [ ERROR ] skipped  skipped 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  ERROR  skipped  skipped 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  ERROR  skipped  skipped 
pitt Mac OS X Leopard (10.5.8) / i386  ERROR  skipped  skipped 

Summary

Package: ENVISIONQuery
Version: 1.1.2
Command: chmod a+r ENVISIONQuery -R && E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ENVISIONQuery
StartedAt: 2011-07-07 00:04:03 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 00:04:31 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 27.8 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'ENVISIONQuery/DESCRIPTION' ... OK
* preparing 'ENVISIONQuery':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: rJava
Loading required package: XML
Jul 7, 2011 12:04:28 AM ReactomeEnvisionClient findPathAdv
SEVERE: null
com.sun.xml.internal.ws.encoding.soap.DeserializationException: Failed to read a response: javax.xml.bind.UnmarshalException
 - with linked exception:
[javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,4347]
Message: XML document structures must start and end within the same entity.]
	at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:113)
	at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:78)
	at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:107)
	at $Proxy42.findPathAdv(Unknown Source)
	at ReactomeEnvisionClient.findPathAdv(ReactomeEnvisionClient.java:52)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at RJavaTools.invokeMethod(RJavaTools.java:386)
Caused by: javax.xml.bind.UnmarshalException
 - with linked exception:
[javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,4347]
Message: XML document structures must start and end within the same entity.]
	at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.handleStreamException(UnmarshallerImpl.java:415)
	at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:351)
	at com.sun.xml.internal.bind.v2.runtime.BridgeImpl.unmarshal(BridgeImpl.java:109)
	at com.sun.xml.internal.bind.api.Bridge.unmarshal(Bridge.java:222)
	at com.sun.xml.internal.ws.client.sei.ResponseBuilder$DocLit.readResponse(ResponseBuilder.java:514)
	at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:110)
	... 9 more
Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,4347]
Message: XML document structures must start and end within the same entity.
	at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:588)
	at com.sun.xml.internal.ws.util.xml.XMLStreamReaderFilter.next(XMLStreamReaderFilter.java:81)
	at com.sun.xml.internal.bind.v2.runtime.unmarshaller.StAXStreamConnector.bridge(StAXStreamConnector.java:181)
	at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:349)
	... 13 more

Error: processing vignette 'ENVISIONQuery.Rnw' failed with diagnostics:
 chunk 2 (label = chunk2) 
Error : Error: com.sun.xml.internal.ws.encoding.soap.DeserializationException: Failed to read a response: javax.xml.bind.UnmarshalException
 - with linked exception:
[javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,4347]
Message: XML document structures must start and end within the same entity.]  does not seem to be XML, nor to identify a file name
Execution halted