Package: RCytoscape

Version: 1.2.1

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.2.1.tar.gz

StartedAt: 2011-10-20 14:08:44 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:31:35 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 1371.2 seconds

RetCode: 1

Status:  ERROR

CheckDir: RCytoscape.Rcheck

Warnings: NA

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/RCytoscape.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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	0.076	0.004	0.117
CytoscapeConnectionClass-class	0.004	0.000	0.001
CytoscapeWindow	0.056	0.000	0.083
CytoscapeWindowClass-class	0.092	0.004	0.202
addCyEdge	0.448	0.004	3.775
addCyNode	0.324	0.004	4.675
addGraphToGraph	0.472	0.000	5.997
clearMsg	0.012	0.000	0.011
clearSelection	0.396	0.020	3.556
copyVisualStyle	0.412	0.040	5.688
createWindowFromSelection	1.300	0.024	5.281
cy2.edge.names	0.020	0.000	0.019
deleteAllWindows	0.316	0.000	1.171
deleteEdgeAttribute	0.320	0.000	5.717
deleteNodeAttribute	0.320	0.004	3.605
deleteSelectedEdges	0.348	0.004	3.675
deleteSelectedNodes	0.344	0.004	3.677
deleteWindow	0.424	0.012	3.823
displayGraph	0.312	0.008	4.654
dockPanel	0.024	0.000	0.038
eda	0.020	0.000	0.021
eda.names	0.020	0.000	0.017
existing.CytoscapeWindow	1.120	0.028	4.283
fitContent	0.340	0.008	4.691
fitSelectedContent	0.368	0.008	4.693
floatPanel	0.024	0.000	0.073
getAllEdgeAttributes	0.308	0.008	4.592
getAllEdges	0.084	0.000	0.111
getAllNodeAttributes	0.300	0.008	4.597
getAllNodes	0.100	0.004	0.147
getArrowShapes	0.016	0.000	0.019
getAttributeClassNames	0.000	0.000	0.001
getCenter	0.304	0.008	4.605
getDefaultBackgroundColor	0.012	0.000	0.011
getDefaultEdgeReverseSelectionColor	0.012	0.000	0.014
getDefaultEdgeSelectionColor	0.012	0.000	0.011
getDefaultNodeReverseSelectionColor	0.012	0.000	0.011
getDefaultNodeSelectionColor	0.012	0.000	0.011
getDirectlyModifiableVisualProperties	0.020	0.000	0.022
getEdgeAttribute	0.332	0.004	4.659
getEdgeAttributeNames	0.012	0.000	0.013
getEdgeCount	0.320	0.004	3.631
getFirstNeighbors	0.360	0.012	3.660
getGraph	0.112	0.000	0.141
getGraphFromCyWindow	1.132	0.020	4.835
getLayoutNameMapping	0.028	0.000	0.030
getLayoutNames	0.012	0.000	0.017
getLayoutPropertyNames	0.016	0.000	0.015
getLayoutPropertyType	0.104	0.004	0.111
getLayoutPropertyValue	0.112	0.000	0.121
getLineStyles	0.012	0.000	0.013
getNodeAttribute	0.336	0.004	3.618
getNodeAttributeNames	0.012	0.000	0.012
getNodeCount	0.340	0.004	3.619
getNodeShapes	0.012	0.000	0.013
getPosition	0.340	0.000	4.618
getSelectedEdgeCount	0.400	0.000	3.732
getSelectedEdges	0.376	0.000	4.648
getSelectedNodeCount	0.400	0.000	3.699
getSelectedNodes	0.405	0.004	4.705
getViewCoordinates	0.380	0.004	5.680
getVisualStyleNames	0.012	0.000	0.015
getWindowCount	0.300	0.012	0.385
getWindowID	0.444	0.004	5.566
getWindowList	0.104	0.000	0.106
getZoom	0.508	0.008	3.829
hideAllPanels	0.248	0.016	0.343
hideNodes	0.188	0.008	0.253
hidePanel	0.028	0.000	0.026
hideSelectedEdges	0.204	0.004	0.507
hideSelectedNodes	0.240	0.008	0.524
initEdgeAttribute	0.004	0.000	0.014
initNodeAttribute	0.004	0.000	0.003
invertEdgeSelection	0.168	0.000	0.240
invertNodeSelection	0.200	0.000	0.293
layout	0.356	0.000	3.709
lockNodeDimensions	0.448	0.004	4.747
makeRandomGraph	0.020	0.000	0.022
makeSimpleGraph	0.028	0.000	0.026
msg	0.012	0.000	0.013
new.CytoscapeWindow	0.144	0.000	0.175
noa	0.016	0.004	0.018
noa.names	0.02	0.00	0.02
ping	0.008	0.000	0.015
raiseWindow	0.172	0.004	0.215
redraw	0.188	0.000	0.230
saveImage	0.372	0.008	3.663
saveNetwork	0.416	0.012	4.769
selectEdges	0.484	0.004	3.826
selectFirstNeighborsOfSelectedNodes	0.548	0.004	5.847
selectNodes	0.232	0.000	0.259
sendEdges	0.204	0.008	2.236
sendNodes	0.176	0.000	0.211
setCenter	0.480	0.048	9.861
setDefaultBackgroundColor	0.012	0.004	0.024
setDefaultEdgeColor	0.444	0.008	3.822
setDefaultEdgeLineWidth	0.428	0.000	4.167
setDefaultEdgeReverseSelectionColor	0.012	0.000	0.027
setDefaultEdgeSelectionColor	0.008	0.000	0.025
setDefaultNodeBorderColor	0.428	0.000	4.057
setDefaultNodeBorderWidth	0.428	0.000	4.115
setDefaultNodeColor	0.408	0.004	3.974
setDefaultNodeFontSize	0.412	0.012	4.139
setDefaultNodeLabelColor	0.420	0.000	5.027
setDefaultNodeReverseSelectionColor	0.008	0.000	0.024
setDefaultNodeSelectionColor	0.012	0.000	0.024
setDefaultNodeShape	0.428	0.008	4.169
setDefaultNodeSize	0.424	0.016	4.191
setEdgeAttributes	0.268	0.000	2.558
setEdgeAttributesDirect	0.228	0.000	1.254
setEdgeColorDirect	0.448	0.000	4.855
setEdgeColorRule	0.408	0.016	4.434
setEdgeFontSizeDirect	1.196	0.056	7.043
setEdgeLabelColorDirect	0.520	0.040	6.116
setEdgeLabelDirect	1.060	0.012	4.407
setEdgeLabelOpacityDirect	1.205	0.020	5.553
setEdgeLabelRule	0.496	0.000	4.801
setEdgeLabelWidthDirect	1.112	0.012	4.581
setEdgeLineStyleDirect	1.184	0.012	4.658
setEdgeLineStyleRule	0.264	0.000	2.296
setEdgeLineWidthDirect	0.820	0.016	4.205
setEdgeLineWidthRule	0.484	0.004	4.797
setEdgeOpacityDirect	1.296	0.032	5.801
setEdgeSourceArrowColorDirect	0.824	0.012	11.198
setEdgeSourceArrowColorRule	0.348	0.004	1.393
setEdgeSourceArrowOpacityDirect	0.936	0.012	12.402
setEdgeSourceArrowRule	0.384	0.000	1.412
setEdgeSourceArrowShapeDirect	0.904	0.032	14.404
setEdgeTargetArrowColorDirect	0.684	0.004	11.244
setEdgeTargetArrowColorRule	0.276	0.004	1.330
setEdgeTargetArrowOpacityDirect	0.916	0.016	6.305
setEdgeTargetArrowRule	0.276	0.000	1.341
setEdgeTargetArrowShapeDirect	0.952	0.024	13.513
setEdgeTooltipDirect	0.612	0.016	4.991
setEdgeTooltipRule	0.500	0.004	5.905
setGraph	0.268	0.000	0.291
setLayoutProperties	0.056	0.000	0.060
setNodeAttributes	0.344	0.000	0.376
setNodeBorderColorRule	0.340	0.012	2.384
setNodeBorderOpacityDirect	0.560	0.000	3.851
setNodeBorderWidthRule	0.533	0.004	6.831
setNodeColorDirect	0.524	0.016	3.921
setNodeColorRule	0.360	0.008	2.403
setNodeFillOpacityDirect	0.512	0.004	4.956
setNodeFontSizeDirect	0.528	0.020	3.854
setNodeHeightDirect	0.540	0.008	3.897
setNodeImageDirect	0.604	0.000	4.234
setNodeLabelDirect	0.560	0.004	3.988
setNodeLabelOpacityDirect	0.568	0.020	4.024
setNodeLabelRule	0.680	0.008	4.034
setNodeOpacityDirect	0.668	0.004	5.960
setNodeShapeDirect	0.552	0.016	5.069
setNodeShapeRule	0.372	0.004	1.412
setNodeSizeDirect	0.568	0.008	3.982
setNodeSizeRule	0.648	0.004	9.001
setNodeTooltipRule	0.588	0.000	8.917
setNodeWidthDirect	0.584	0.000	4.046
setNotAttributesDirect	0.364	0.000	0.436
setPosition	0.552	0.004	5.968
setVisualStyle	0.748	0.000	7.606
setWindowSize	0.640	0.028	6.146
setZoom	0.628	0.048	6.042
showGraphicsDetails	0.012	0.000	0.014
unhideAll	0.648	0.012	6.001
unhideNodes	0.424	0.016	1.467
validCyWin	0.364	0.004	0.387
version	0.012	0.000	0.011