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 |
* 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