BioC 2.9: CHECK report for RCytoscape on wilson2

Package: RCytoscape

Version: 1.3.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.3.0.tar.gz

StartedAt: 2011-05-09 13:54:07 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:16:16 -0700 (Mon, 09 May 2011)

EllapsedTime: 1328.7 seconds

RetCode: 0

Status: OK

CheckDir: RCytoscape.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/RCytoscape.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.3.0’
* checking package name space 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘RCytoscape’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘RCytoscape.Rnw’ 
** testing if installed package can be loaded

* DONE (RCytoscape)

name	user	system	elapsed
CytoscapeConnection	0.072	0.008	0.153
CytoscapeConnectionClass-class	0.000	0.000	0.001
CytoscapeWindow	0.048	0.004	0.093
CytoscapeWindowClass-class	0.092	0.000	0.149
addCyEdge	0.400	0.004	3.849
addCyNode	0.392	0.000	4.803
addGraphToGraph	0.532	0.004	5.065
clearMsg	0.008	0.000	0.012
clearSelection	0.340	0.012	4.479
copyVisualStyle	0.380	0.008	4.706
createWindowFromSelection	1.404	0.036	5.055
cy2.edge.names	0.020	0.000	0.021
deleteAllWindows	0.308	0.004	1.135
deleteEdgeAttribute	0.296	0.008	3.578
deleteNodeAttribute	0.296	0.004	3.593
deleteSelectedEdges	0.328	0.008	3.624
deleteSelectedNodes	0.316	0.016	3.595
deleteWindow	0.404	0.008	5.776
displayGraph	0.292	0.008	4.557
dockPanel	0.024	0.000	0.028
eda	0.016	0.004	0.017
eda.names	0.020	0.000	0.021
existing.CytoscapeWindow	1.016	0.020	4.118
fitContent	0.348	0.004	4.689
fitSelectedContent	0.384	0.004	4.654
floatPanel	0.024	0.000	0.067
getAllEdgeAttributes	0.320	0.004	3.652
getAllEdges	0.084	0.004	0.108
getAllNodeAttributes	0.328	0.004	4.594
getAllNodes	0.104	0.000	0.128
getArrowShapes	0.016	0.000	0.012
getAttributeClassNames	0.000	0.000	0.001
getCenter	0.340	0.004	3.635
getDefaultBackgroundColor	0.012	0.000	0.011
getDefaultEdgeReverseSelectionColor	0.012	0.000	0.011
getDefaultEdgeSelectionColor	0.008	0.000	0.011
getDefaultNodeReverseSelectionColor	0.008	0.004	0.013
getDefaultNodeSelectionColor	0.012	0.000	0.014
getDirectlyModifiableVisualProperties	0.020	0.000	0.023
getEdgeAttribute	0.356	0.004	3.621
getEdgeAttributeNames	0.012	0.000	0.012
getEdgeCount	0.348	0.004	4.616
getFirstNeighbors	0.376	0.016	4.684
getGraph	0.196	0.000	0.215
getGraphFromCyWindow	1.052	0.008	5.402
getLayoutNameMapping	0.020	0.004	0.028
getLayoutNames	0.008	0.000	0.014
getLayoutPropertyNames	0.012	0.000	0.014
getLayoutPropertyType	0.096	0.004	0.105
getLayoutPropertyValue	0.096	0.000	0.103
getLineStyles	0.012	0.000	0.014
getNodeAttribute	0.332	0.008	4.645
getNodeAttributeNames	0.008	0.000	0.012
getNodeCount	0.324	0.004	3.633
getNodeShapes	0.012	0.000	0.014
getPosition	0.344	0.008	3.629
getSelectedEdgeCount	0.364	0.012	3.776
getSelectedEdges	0.336	0.012	3.616
getSelectedNodeCount	0.436	0.008	4.706
getSelectedNodes	0.404	0.004	3.670
getViewCoordinates	0.349	0.000	3.641
getVisualStyleNames	0.004	0.008	0.013
getWindowCount	0.276	0.000	0.334
getWindowID	0.428	0.004	4.494
getWindowList	0.104	0.000	0.106
getZoom	0.356	0.008	4.662
hideAllPanels	0.264	0.004	0.360
hideNodes	0.200	0.000	0.231
hidePanel	0.024	0.000	0.025
hideSelectedEdges	0.212	0.000	0.490
hideSelectedNodes	0.228	0.012	0.515
initEdgeAttribute	0.004	0.000	0.005
initNodeAttribute	0.004	0.000	0.003
invertEdgeSelection	0.188	0.000	0.238
invertNodeSelection	0.208	0.000	0.242
layout	0.392	0.000	3.707
lockNodeDimensions	0.472	0.008	3.744
makeRandomGraph	0.02	0.00	0.02
makeSimpleGraph	0.024	0.000	0.024
msg	0.012	0.000	0.012
new.CytoscapeWindow	0.144	0.000	0.168
noa	0.020	0.000	0.019
noa.names	0.016	0.000	0.015
ping	0.012	0.000	0.011
raiseWindow	0.164	0.000	0.185
redraw	0.168	0.000	0.191
saveImage	0.392	0.000	4.668
saveNetwork	0.472	0.004	4.867
selectEdges	0.452	0.016	4.809
selectFirstNeighborsOfSelectedNodes	0.640	0.028	3.953
selectNodes	0.228	0.012	0.265
sendEdges	0.212	0.004	1.237
sendNodes	0.184	0.000	0.209
setCenter	0.484	0.052	8.819
setDefaultBackgroundColor	0.012	0.000	0.013
setDefaultEdgeColor	0.424	0.008	3.700
setDefaultEdgeLineWidth	0.400	0.000	3.873
setDefaultEdgeReverseSelectionColor	0.012	0.000	0.027
setDefaultEdgeSelectionColor	0.012	0.000	0.028
setDefaultNodeBorderColor	0.388	0.000	4.079
setDefaultNodeBorderWidth	0.392	0.004	4.057
setDefaultNodeColor	0.376	0.012	4.057
setDefaultNodeFontSize	0.396	0.000	4.183
setDefaultNodeLabelColor	0.404	0.004	5.071
setDefaultNodeReverseSelectionColor	0.008	0.000	0.027
setDefaultNodeSelectionColor	0.012	0.000	0.024
setDefaultNodeShape	0.432	0.008	4.172
setDefaultNodeSize	0.408	0.004	5.094
setEdgeAttributes	0.256	0.000	3.547
setEdgeAttributesDirect	0.208	0.004	1.460
setEdgeColorDirect	0.432	0.008	4.494
setEdgeColorRule	0.308	0.012	4.211
setEdgeFontSizeDirect	1.264	0.040	4.838
setEdgeLabelColorDirect	0.548	0.016	3.916
setEdgeLabelDirect	1.104	0.032	4.478
setEdgeLabelOpacityDirect	1.169	0.024	5.653
setEdgeLabelRule	0.448	0.012	3.811
setEdgeLabelWidthDirect	1.120	0.012	5.580
setEdgeLineStyleDirect	1.272	0.020	5.661
setEdgeLineStyleRule	0.268	0.000	1.295
setEdgeLineWidthDirect	0.792	0.016	4.121
setEdgeLineWidthRule	0.472	0.012	5.780
setEdgeOpacityDirect	1.156	0.032	4.700
setEdgeSourceArrowColorDirect	0.684	0.008	10.041
setEdgeSourceArrowColorRule	0.260	0.000	1.334
setEdgeSourceArrowOpacityDirect	0.888	0.016	11.238
setEdgeSourceArrowRule	0.272	0.000	1.306
setEdgeSourceArrowShapeDirect	0.940	0.024	13.303
setEdgeTargetArrowColorDirect	0.704	0.004	10.092
setEdgeTargetArrowColorRule	0.280	0.000	1.307
setEdgeTargetArrowOpacityDirect	0.912	0.016	4.280
setEdgeTargetArrowRule	0.300	0.000	1.339
setEdgeTargetArrowShapeDirect	0.952	0.016	13.335
setEdgeTooltipDirect	0.652	0.012	6.957
setEdgeTooltipRule	0.524	0.012	5.939
setGraph	0.308	0.000	0.335
setLayoutProperties	0.056	0.000	0.060
setNodeAttributes	0.388	0.000	0.421
setNodeBorderColorRule	0.464	0.012	2.519
setNodeBorderOpacityDirect	0.512	0.008	3.849
setNodeBorderWidthRule	0.500	0.008	4.829
setNodeColorDirect	0.524	0.004	3.856
setNodeColorRule	0.365	0.000	2.424
setNodeFillOpacityDirect	0.548	0.004	4.033
setNodeFontSizeDirect	0.544	0.004	3.869
setNodeHeightDirect	0.560	0.004	5.908
setNodeImageDirect	0.576	0.008	5.010
setNodeLabelDirect	0.560	0.004	5.014
setNodeLabelOpacityDirect	0.580	0.000	4.902
setNodeLabelRule	0.704	0.004	4.122
setNodeOpacityDirect	0.620	0.008	5.020
setNodeShapeDirect	0.584	0.012	5.064
setNodeShapeRule	0.368	0.008	1.443
setNodeSizeDirect	0.576	0.000	3.915
setNodeSizeRule	0.652	0.012	9.967
setNodeTooltipRule	0.616	0.008	6.913
setNodeWidthDirect	0.568	0.016	5.000
setNotAttributesDirect	0.356	0.004	0.396
setPosition	0.568	0.004	4.895
setVisualStyle	0.808	0.008	8.371
setWindowSize	0.632	0.024	7.149
setZoom	0.580	0.044	5.934
showGraphicsDetails	0.012	0.000	0.013
unhideAll	0.616	0.008	3.909
unhideNodes	0.404	0.028	1.461
validCyWin	0.344	0.000	0.383
version	0.008	0.000	0.011

Summary

Command output