Package: RCytoscape

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RCytoscape_1.2.1.tar.gz

StartedAt: 2011-10-20 16:51:55 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:24:54 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 1979.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: RCytoscape.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/RCytoscape.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under inst/doc ... 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	0.100	0.003	0.203
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.075	0.002	0.135
CytoscapeWindowClass-class	0.122	0.002	0.178
addCyEdge	0.517	0.013	6.948
addCyNode	0.412	0.010	6.745
addGraphToGraph	0.586	0.014	9.203
clearMsg	0.014	0.001	0.016
clearSelection	0.447	0.012	6.535
copyVisualStyle	0.529	0.017	8.054
createWindowFromSelection	1.698	0.044	8.964
cy2.edge.names	0.028	0.000	0.029
deleteAllWindows	0.393	0.010	1.449
deleteEdgeAttribute	0.414	0.010	6.723
deleteNodeAttribute	0.411	0.009	6.692
deleteSelectedEdges	0.442	0.010	6.723
deleteSelectedNodes	0.426	0.009	6.744
deleteWindow	0.530	0.013	6.920
displayGraph	0.387	0.010	6.711
dockPanel	0.028	0.001	0.036
eda	0.024	0.001	0.025
eda.names	0.029	0.000	0.029
existing.CytoscapeWindow	1.403	0.038	7.594
fitContent	0.444	0.012	6.747
fitSelectedContent	0.494	0.013	6.961
floatPanel	0.027	0.001	0.114
getAllEdgeAttributes	0.397	0.009	6.745
getAllEdges	0.114	0.002	0.158
getAllNodeAttributes	0.403	0.008	6.721
getAllNodes	0.128	0.002	0.176
getArrowShapes	0.018	0.001	0.020
getAttributeClassNames	0.001	0.000	0.002
getCenter	0.417	0.008	6.720
getDefaultBackgroundColor	0.014	0.000	0.025
getDefaultEdgeReverseSelectionColor	0.013	0.000	0.016
getDefaultEdgeSelectionColor	0.013	0.001	0.016
getDefaultNodeReverseSelectionColor	0.017	0.001	0.018
getDefaultNodeSelectionColor	0.013	0.001	0.017
getDirectlyModifiableVisualProperties	0.029	0.001	0.033
getEdgeAttribute	0.437	0.010	6.746
getEdgeAttributeNames	0.015	0.001	0.018
getEdgeCount	0.430	0.010	6.737
getFirstNeighbors	0.486	0.011	6.776
getGraph	0.139	0.002	0.172
getGraphFromCyWindow	1.443	0.033	7.894
getLayoutNameMapping	0.049	0.001	0.052
getLayoutNames	0.017	0.001	0.020
getLayoutPropertyNames	0.017	0.001	0.018
getLayoutPropertyType	0.130	0.004	0.144
getLayoutPropertyValue	0.146	0.005	0.169
getLineStyles	0.019	0.001	0.026
getNodeAttribute	0.448	0.009	6.763
getNodeAttributeNames	0.021	0.001	0.024
getNodeCount	0.470	0.010	6.759
getNodeShapes	0.019	0.001	0.021
getPosition	0.446	0.009	6.727
getSelectedEdgeCount	0.498	0.011	6.789
getSelectedEdges	0.465	0.009	6.799
getSelectedNodeCount	0.505	0.010	6.807
getSelectedNodes	0.525	0.010	6.817
getViewCoordinates	0.478	0.009	6.762
getVisualStyleNames	0.021	0.001	0.025
getWindowCount	0.431	0.008	0.498
getWindowID	0.592	0.010	6.657
getWindowList	0.136	0.002	0.141
getZoom	0.557	0.011	6.888
hideAllPanels	0.325	0.015	0.456
hideNodes	0.259	0.005	0.310
hidePanel	0.026	0.001	0.029
hideSelectedEdges	0.281	0.006	0.595
hideSelectedNodes	0.316	0.006	0.615
initEdgeAttribute	0.004	0.000	0.003
initNodeAttribute	0.003	0.000	0.003
invertEdgeSelection	0.236	0.003	0.270
invertNodeSelection	0.286	0.005	0.324
layout	0.487	0.009	6.844
lockNodeDimensions	0.572	0.012	7.011
makeRandomGraph	0.022	0.000	0.022
makeSimpleGraph	0.030	0.001	0.030
msg	0.014	0.001	0.016
new.CytoscapeWindow	0.200	0.003	0.254
noa	0.024	0.001	0.028
noa.names	0.026	0.000	0.026
ping	0.012	0.000	0.019
raiseWindow	0.238	0.004	0.294
redraw	0.236	0.003	0.270
saveImage	0.512	0.009	6.849
saveNetwork	0.505	0.008	6.786
selectEdges	0.605	0.011	6.918
selectFirstNeighborsOfSelectedNodes	0.711	0.015	7.084
selectNodes	0.316	0.004	0.360
sendEdges	0.285	0.003	2.316
sendNodes	0.271	0.004	0.305
setCenter	0.674	0.078	12.177
setDefaultBackgroundColor	0.014	0.001	0.018
setDefaultEdgeColor	0.570	0.014	7.098
setDefaultEdgeLineWidth	0.572	0.009	7.539
setDefaultEdgeReverseSelectionColor	0.016	0.001	0.027
setDefaultEdgeSelectionColor	0.014	0.000	0.035
setDefaultNodeBorderColor	0.575	0.010	7.397
setDefaultNodeBorderWidth	0.584	0.010	7.270
setDefaultNodeColor	0.584	0.009	7.308
setDefaultNodeFontSize	0.591	0.009	7.353
setDefaultNodeLabelColor	0.591	0.011	7.379
setDefaultNodeReverseSelectionColor	0.018	0.001	0.058
setDefaultNodeSelectionColor	0.016	0.001	0.021
setDefaultNodeShape	0.611	0.010	7.189
setDefaultNodeSize	0.602	0.010	6.966
setEdgeAttributes	0.376	0.005	4.406
setEdgeAttributesDirect	0.329	0.004	2.383
setEdgeColorDirect	0.628	0.010	6.973
setEdgeColorRule	0.504	0.013	7.602
setEdgeFontSizeDirect	1.561	0.038	8.068
setEdgeLabelColorDirect	0.704	0.013	7.026
setEdgeLabelDirect	1.407	0.031	7.937
setEdgeLabelOpacityDirect	1.410	0.031	7.869
setEdgeLabelRule	0.613	0.009	6.909
setEdgeLabelWidthDirect	1.529	0.043	8.019
setEdgeLineStyleDirect	1.611	0.045	8.964
setEdgeLineStyleRule	0.377	0.004	2.414
setEdgeLineWidthDirect	1.091	0.023	7.491
setEdgeLineWidthRule	0.654	0.009	8.761
setEdgeOpacityDirect	1.491	0.035	7.948
setEdgeSourceArrowColorDirect	0.929	0.019	15.292
setEdgeSourceArrowColorRule	0.384	0.004	2.429
setEdgeSourceArrowOpacityDirect	1.225	0.029	14.715
setEdgeSourceArrowRule	0.457	0.004	2.493
setEdgeSourceArrowShapeDirect	1.259	0.033	16.755
setEdgeTargetArrowColorDirect	0.926	0.017	15.321
setEdgeTargetArrowColorRule	0.389	0.003	2.424
setEdgeTargetArrowOpacityDirect	1.225	0.024	7.701
setEdgeTargetArrowRule	0.413	0.004	2.502
setEdgeTargetArrowShapeDirect	1.274	0.026	16.839
setEdgeTooltipDirect	0.838	0.015	8.319
setEdgeTooltipRule	0.708	0.012	9.102
setGraph	0.398	0.003	0.425
setLayoutProperties	0.077	0.002	0.096
setNodeAttributes	0.491	0.005	0.538
setNodeBorderColorRule	0.491	0.006	4.544
setNodeBorderOpacityDirect	0.719	0.010	7.039
setNodeBorderWidthRule	0.716	0.010	9.128
setNodeColorDirect	0.732	0.011	7.047
setNodeColorRule	0.516	0.006	4.580
setNodeFillOpacityDirect	0.735	0.011	7.077
setNodeFontSizeDirect	0.735	0.012	7.044
setNodeHeightDirect	0.783	0.017	7.201
setNodeImageDirect	0.792	0.011	7.142
setNodeLabelDirect	0.757	0.010	6.087
setNodeLabelOpacityDirect	0.743	0.009	7.081
setNodeLabelRule	0.930	0.014	7.401
setNodeOpacityDirect	0.801	0.011	7.141
setNodeShapeDirect	0.841	0.012	7.236
setNodeShapeRule	0.511	0.005	2.667
setNodeSizeDirect	0.758	0.009	6.090
setNodeSizeRule	0.888	0.014	13.349
setNodeTooltipRule	0.841	0.013	13.229
setNodeWidthDirect	0.799	0.012	7.117
setNotAttributesDirect	0.493	0.005	0.540
setPosition	0.773	0.012	9.096
setVisualStyle	0.965	0.017	11.099
setWindowSize	0.880	0.050	9.293
setZoom	0.851	0.057	8.228
showGraphicsDetails	0.017	0.003	0.023
unhideAll	0.887	0.027	7.402
unhideNodes	0.611	0.027	1.697
validCyWin	0.493	0.013	0.561
version	0.013	0.001	0.014