BioC 2.8: CHECK report for RCytoscape on liverpool

Package: RCytoscape

Version: 1.2.1

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch RCytoscape_1.2.1.tar.gz

StartedAt: 2011-10-20 16:34:31 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:07:10 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 1959.0 seconds

RetCode: 1

Status: ERROR

CheckDir: RCytoscape.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/RCytoscape.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RCytoscape/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCytoscape' version '1.2.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RCytoscape' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'RCytoscape_unit_tests.R'
 ERROR
Running the tests in 'tests/RCytoscape_unit_tests.R' failed.
Last 13 lines of output:
  1 Test Suite : 
  RCytoscape RUnit Tests - 130 test functions, 1 error, 0 failures
  ERROR in test.getPosition: Error in convertToR(xmlParse(node, asText = TRUE)) : 
    faultCode: 0 faultString: Failed to parse XML-RPC request: Failed to parse double value: NA
  
  Test files with failing tests
  
     test_cytoscape.R 
       test.getPosition 
  
  
  Error in RCytoscape:::.test() : unit tests failed for package RCytoscape
  Execution halted

* installing *source* package 'RCytoscape' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RCytoscape)

name	user	system	elapsed
CytoscapeConnection	0.16	0.00	0.40
CytoscapeConnectionClass-class	0	0	0
CytoscapeWindow	0.03	0.00	0.11
CytoscapeWindowClass-class	0.11	0.00	0.18
addCyEdge	0.39	0.00	6.77
addCyNode	0.29	0.00	6.70
addGraphToGraph	0.41	0.00	9.08
clearMsg	0.02	0.00	0.02
clearSelection	0.26	0.01	5.56
copyVisualStyle	0.33	0.00	7.80
createWindowFromSelection	1.05	0.07	9.11
cy2.edge.names	0.02	0.00	0.02
deleteAllWindows	0.36	0.00	1.48
deleteEdgeAttribute	0.25	0.00	6.80
deleteNodeAttribute	0.25	0.01	6.83
deleteSelectedEdges	0.30	0.02	6.74
deleteSelectedNodes	0.26	0.01	6.76
deleteWindow	0.33	0.02	6.96
displayGraph	0.28	0.01	6.73
dockPanel	0.02	0.00	0.06
eda	0.02	0.02	0.03
eda.names	0.01	0.00	0.02
existing.CytoscapeWindow	0.78	0.09	7.81
fitContent	0.28	0.02	6.75
fitSelectedContent	0.28	0.00	6.78
floatPanel	0.02	0.00	0.11
getAllEdgeAttributes	0.23	0.05	6.77
getAllEdges	0.07	0.00	0.12
getAllNodeAttributes	0.28	0.00	6.64
getAllNodes	0.09	0.00	0.14
getArrowShapes	0.00	0.00	0.02
getAttributeClassNames	0	0	0
getCenter	0.28	0.00	6.78
getDefaultBackgroundColor	0.00	0.00	0.03
getDefaultEdgeReverseSelectionColor	0.02	0.00	0.03
getDefaultEdgeSelectionColor	0.00	0.00	0.02
getDefaultNodeReverseSelectionColor	0.01	0.00	0.01
getDefaultNodeSelectionColor	0.02	0.00	0.02
getDirectlyModifiableVisualProperties	0.02	0.00	0.03
getEdgeAttribute	0.29	0.01	6.72
getEdgeAttributeNames	0.00	0.00	0.02
getEdgeCount	0.28	0.02	6.71
getFirstNeighbors	0.35	0.00	6.82
getGraph	0.09	0.00	0.17
getGraphFromCyWindow	0.97	0.03	8.05
getLayoutNameMapping	0.05	0.00	0.06
getLayoutNames	0.00	0.00	0.01
getLayoutPropertyNames	0.03	0.00	0.04
getLayoutPropertyType	0.08	0.00	0.20
getLayoutPropertyValue	0.06	0.00	0.15
getLineStyles	0.01	0.00	0.02
getNodeAttribute	0.32	0.00	6.78
getNodeAttributeNames	0.00	0.00	0.02
getNodeCount	0.29	0.00	6.70
getNodeShapes	0.02	0.00	0.02
getPosition	0.33	0.00	6.75
getSelectedEdgeCount	0.34	0.01	6.84
getSelectedEdges	0.27	0.00	6.67
getSelectedNodeCount	0.37	0.00	6.85
getSelectedNodes	0.35	0.04	9.85
getViewCoordinates	0.34	0.00	6.80
getVisualStyleNames	0.02	0.00	0.02
getWindowCount	0.25	0.00	0.37
getWindowID	0.37	0.01	6.58
getWindowList	0.09	0.00	0.11
getZoom	0.43	0.00	6.84
hideAllPanels	0.23	0.00	0.47
hideNodes	0.16	0.02	0.30
hidePanel	0.00	0.00	0.03
hideSelectedEdges	0.18	0.00	0.55
hideSelectedNodes	0.18	0.01	0.59
initEdgeAttribute	0	0	0
initNodeAttribute	0	0	0
invertEdgeSelection	0.17	0.00	0.25
invertNodeSelection	0.15	0.00	0.30
layout	0.30	0.02	6.79
lockNodeDimensions	0.31	0.03	6.83
makeRandomGraph	0.02	0.00	0.02
makeSimpleGraph	0.03	0.00	0.03
msg	0.00	0.00	0.02
new.CytoscapeWindow	0.13	0.00	0.21
noa	0.01	0.00	0.02
noa.names	0.02	0.00	0.02
ping	0.01	0.00	0.01
raiseWindow	0.16	0.00	0.24
redraw	0.14	0.01	0.21
saveImage	0.36	0.02	6.82
saveNetwork	0.34	0.00	6.82
selectEdges	0.42	0.02	7.10
selectFirstNeighborsOfSelectedNodes	0.46	0.00	7.06
selectNodes	0.22	0.00	0.33
sendEdges	0.20	0.00	2.28
sendNodes	0.2	0.0	0.3
setCenter	0.41	0.00	12.92
setDefaultBackgroundColor	0.00	0.00	0.05
setDefaultEdgeColor	0.37	0.00	6.86
setDefaultEdgeLineWidth	0.44	0.00	6.87
setDefaultEdgeReverseSelectionColor	0.00	0.00	0.02
setDefaultEdgeSelectionColor	0.00	0.00	0.01
setDefaultNodeBorderColor	0.36	0.00	6.94
setDefaultNodeBorderWidth	0.38	0.03	6.89
setDefaultNodeColor	0.35	0.00	6.89
setDefaultNodeFontSize	0.36	0.00	6.88
setDefaultNodeLabelColor	0.41	0.00	6.78
setDefaultNodeReverseSelectionColor	0.00	0.01	0.03
setDefaultNodeSelectionColor	0.00	0.00	0.03
setDefaultNodeShape	0.41	0.00	6.94
setDefaultNodeSize	0.37	0.03	7.26
setEdgeAttributes	0.27	0.02	4.42
setEdgeAttributesDirect	0.20	0.00	2.29
setEdgeColorDirect	0.44	0.00	7.01
setEdgeColorRule	0.39	0.02	7.22
setEdgeFontSizeDirect	0.94	0.04	8.92
setEdgeLabelColorDirect	0.42	0.03	7.17
setEdgeLabelDirect	0.76	0.08	8.08
setEdgeLabelOpacityDirect	0.91	0.05	7.92
setEdgeLabelRule	0.45	0.01	6.82
setEdgeLabelWidthDirect	0.99	0.07	7.86
setEdgeLineStyleDirect	0.93	0.06	8.18
setEdgeLineStyleRule	0.24	0.00	2.33
setEdgeLineWidthDirect	0.67	0.01	7.38
setEdgeLineWidthRule	0.42	0.00	8.81
setEdgeOpacityDirect	0.92	0.03	8.05
setEdgeSourceArrowColorDirect	0.65	0.00	15.16
setEdgeSourceArrowColorRule	0.26	0.00	2.36
setEdgeSourceArrowOpacityDirect	0.67	0.02	14.67
setEdgeSourceArrowRule	0.32	0.00	2.42
setEdgeSourceArrowShapeDirect	0.70	0.01	16.81
setEdgeTargetArrowColorDirect	0.59	0.00	15.30
setEdgeTargetArrowColorRule	0.27	0.00	2.36
setEdgeTargetArrowOpacityDirect	0.86	0.02	7.67
setEdgeTargetArrowRule	0.31	0.00	2.34
setEdgeTargetArrowShapeDirect	0.67	0.09	16.80
setEdgeTooltipDirect	0.55	0.03	8.16
setEdgeTooltipRule	0.45	0.00	9.00
setGraph	0.28	0.00	0.42
setLayoutProperties	0.02	0.00	0.12
setNodeAttributes	0.33	0.00	0.47
setNodeBorderColorRule	0.29	0.00	4.46
setNodeBorderOpacityDirect	0.44	0.00	6.93
setNodeBorderWidthRule	0.47	0.02	8.93
setNodeColorDirect	0.48	0.00	6.95
setNodeColorRule	0.33	0.00	4.47
setNodeFillOpacityDirect	0.50	0.03	7.12
setNodeFontSizeDirect	0.49	0.02	6.94
setNodeHeightDirect	0.50	0.01	6.95
setNodeImageDirect	0.48	0.00	7.13
setNodeLabelDirect	0.50	0.02	7.15
setNodeLabelOpacityDirect	0.50	0.01	6.97
setNodeLabelRule	0.63	0.02	7.44
setNodeOpacityDirect	0.56	0.01	7.09
setNodeShapeDirect	0.47	0.00	7.19
setNodeShapeRule	0.29	0.02	2.44
setNodeSizeDirect	0.49	0.00	7.05
setNodeSizeRule	0.55	0.00	13.22
setNodeTooltipRule	0.59	0.00	13.03
setNodeWidthDirect	0.55	0.00	7.17
setNotAttributesDirect	0.34	0.00	0.44
setPosition	0.48	0.00	9.00
setVisualStyle	0.72	0.02	10.82
setWindowSize	0.57	0.03	9.57
setZoom	0.57	0.00	9.39
showGraphicsDetails	0.00	0.00	0.01
unhideAll	0.58	0.00	7.07
unhideNodes	0.42	0.01	1.68
validCyWin	0.38	0.00	0.39
version	0.01	0.00	0.03

Summary

Command output