Package: RCytoscape

Version: 1.4.4

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.4.4.tar.gz

StartedAt: 2012-03-24 02:15:22 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:40:06 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 1484.7 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 2.14.2 (2012-02-29)
* 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 ‘1.4.4’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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’
 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
Creating a new generic function for ‘layout’ in package ‘RCytoscape’
** 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	0.044	0.000	0.091
CytoscapeConnectionClass-class	0.004	0.000	0.000
CytoscapeWindow	0.048	0.000	0.092
CytoscapeWindowClass-class	0.076	0.004	0.133
addCyEdge	0.372	0.000	3.725
addCyNode	0.356	0.000	3.640
addGraphToGraph	0.484	0.012	5.005
clearMsg	0.012	0.000	0.011
clearSelection	0.356	0.004	3.440
copyVisualStyle	0.428	0.000	5.903
createWindowFromSelection	1.364	0.028	4.787
cy2.edge.names	0.016	0.000	0.016
deleteAllWindows	0.292	0.000	1.495
deleteEdgeAttribute	0.324	0.004	4.613
deleteNodeAttribute	0.348	0.000	3.680
deleteSelectedEdges	0.368	0.008	3.857
deleteSelectedNodes	0.380	0.004	4.873
deleteWindow	0.416	0.008	5.020
demoSimpleGraph	0.484	0.008	6.813
displayGraph	0.324	0.000	4.621
dockPanel	0.020	0.000	0.036
eda	0.020	0.000	0.021
eda.names	0.012	0.000	0.014
existing.CytoscapeWindow	1.152	0.020	4.261
fitContent	0.404	0.004	3.684
fitSelectedContent	0.436	0.008	3.766
floatPanel	0.024	0.000	0.072
getAllEdgeAttributes	0.332	0.020	3.669
getAllEdges	0.092	0.000	0.116
getAllNodeAttributes	0.360	0.004	3.626
getAllNodes	0.112	0.004	0.138
getArrowShapes	0.012	0.000	0.014
getAttributeClassNames	0.000	0.000	0.001
getCenter	0.400	0.000	4.705
getDefaultBackgroundColor	0.012	0.000	0.012
getDefaultEdgeReverseSelectionColor	0.012	0.000	0.012
getDefaultEdgeSelectionColor	0.020	0.000	0.019
getDefaultNodeReverseSelectionColor	0.012	0.000	0.015
getDefaultNodeSelectionColor	0.012	0.000	0.014
getDirectlyModifiableVisualProperties	0.024	0.000	0.027
getEdgeAttribute	0.468	0.004	6.725
getEdgeAttributeNames	0.004	0.008	0.013
getEdgeCount	0.328	0.008	3.624
getFirstNeighbors	0.388	0.004	3.651
getGraph	0.096	0.000	0.120
getGraphFromCyWindow	1.028	0.012	4.353
getLayoutNameMapping	0.032	0.000	0.031
getLayoutNames	0.012	0.000	0.014
getLayoutPropertyNames	0.016	0.000	0.013
getLayoutPropertyType	0.092	0.000	0.102
getLayoutPropertyValue	0.096	0.004	0.102
getLineStyles	0.016	0.000	0.014
getNodeAttribute	0.340	0.004	4.614
getNodeAttributeNames	0.008	0.000	0.013
getNodeCount	0.352	0.008	3.658
getNodeShapes	0.016	0.000	0.013
getPosition	0.360	0.004	4.621
getSelectedEdgeCount	0.420	0.004	3.681
getSelectedEdges	0.397	0.004	4.658
getSelectedNodeCount	0.444	0.000	3.804
getSelectedNodes	0.472	0.024	3.927
getViewCoordinates	0.388	0.004	3.684
getVisualStyleNames	0.012	0.000	0.019
getWindowCount	0.316	0.000	0.435
getWindowID	0.472	0.004	3.565
getWindowList	0.108	0.000	0.105
getZoom	0.380	0.004	3.669
hideAllPanels	0.300	0.008	0.463
hideNodes	0.248	0.008	0.338
hidePanel	0.028	0.000	0.035
hideSelectedEdges	0.244	0.004	0.667
hideSelectedNodes	0.236	0.008	0.331
initEdgeAttribute	0.004	0.000	0.003
initNodeAttribute	0.000	0.004	0.002
invertEdgeSelection	0.208	0.004	0.276
invertNodeSelection	0.248	0.012	0.393
layout	0.440	0.016	4.854
lockNodeDimensions	0.504	0.012	4.849
makeRandomGraph	0.016	0.000	0.020
makeSimpleGraph	0.028	0.000	0.036
msg	0.012	0.000	0.015
new.CytoscapeWindow	0.152	0.008	0.203
noa	0.020	0.000	0.019
noa.names	0.024	0.000	0.028
ping	0.012	0.000	0.013
raiseWindow	0.188	0.004	0.245
redraw	0.192	0.000	0.245
restoreLayout	0.648	0.016	5.369
saveImage	0.384	0.000	3.662
saveLayout	0.480	0.012	5.976
saveNetwork	0.388	0.008	3.695
selectEdges	0.480	0.028	3.784
selectFirstNeighborsOfSelectedNodes	0.568	0.004	4.846
selectNodes	0.256	0.004	0.285
sendEdges	0.232	0.004	1.260
sendNodes	0.212	0.004	0.237
setCenter	0.556	0.056	9.023
setDefaultBackgroundColor	0.016	0.004	0.034
setDefaultEdgeColor	0.468	0.012	3.746
setDefaultEdgeLineWidth	0.468	0.012	3.740
setDefaultEdgeReverseSelectionColor	0.016	0.000	0.016
setDefaultEdgeSelectionColor	0.012	0.000	0.013
setDefaultNodeBorderColor	0.468	0.012	4.751
setDefaultNodeBorderWidth	0.480	0.016	3.839
setDefaultNodeColor	0.520	0.008	4.794
setDefaultNodeFontSize	0.508	0.000	4.805
setDefaultNodeLabelColor	0.508	0.000	3.884
setDefaultNodeReverseSelectionColor	0.012	0.000	0.013
setDefaultNodeSelectionColor	0.008	0.004	0.013
setDefaultNodeShape	0.512	0.012	4.812
setDefaultNodeSize	0.512	0.000	3.786
setEdgeAttributes	0.308	0.008	2.339
setEdgeAttributesDirect	0.264	0.004	1.426
setEdgeColorDirect	0.532	0.004	3.916
setEdgeColorRule	0.385	0.008	3.431
setEdgeFontSizeDirect	1.424	0.024	5.537
setEdgeLabelColorDirect	0.656	0.012	4.370
setEdgeLabelDirect	1.364	0.032	5.785
setEdgeLabelOpacityDirect	1.116	0.016	4.568
setEdgeLabelRule	0.500	0.004	3.928
setEdgeLabelWidthDirect	1.256	0.068	4.895
setEdgeLineStyleDirect	1.308	0.044	4.765
setEdgeLineStyleRule	0.300	0.004	1.350
setEdgeLineWidthDirect	0.948	0.004	4.252
setEdgeLineWidthRule	0.568	0.008	4.938
setEdgeOpacityDirect	1.216	0.028	28.646
setEdgeSourceArrowColorDirect	0.756	0.020	11.102
setEdgeSourceArrowColorRule	0.308	0.016	1.345
setEdgeSourceArrowOpacityDirect	1.076	0.036	11.432
setEdgeSourceArrowRule	0.300	0.012	1.359
setEdgeSourceArrowShapeDirect	1.084	0.028	13.601
setEdgeTargetArrowColorDirect	0.812	0.008	10.126
setEdgeTargetArrowColorRule	0.308	0.000	1.365
setEdgeTargetArrowOpacityDirect	1.009	0.020	4.369
setEdgeTargetArrowRule	0.284	0.000	1.314
setEdgeTargetArrowShapeDirect	1.008	0.008	13.351
setEdgeTooltipDirect	0.672	0.016	6.185
setEdgeTooltipRule	0.568	0.004	4.848
setGraph	0.260	0.000	0.317
setLayoutProperties	0.056	0.000	0.065
setNodeAttributes	0.332	0.000	0.398
setNodeAttributesDirect	0.300	0.000	0.347
setNodeBorderColorDirect	0.644	0.012	4.974
setNodeBorderColorRule	0.384	0.004	2.428
setNodeBorderOpacityDirect	0.684	0.004	4.106
setNodeBorderWidthDirect	0.740	0.012	4.124
setNodeBorderWidthRule	0.720	0.012	6.000
setNodeColorDirect	0.764	0.008	4.053
setNodeColorRule	0.488	0.008	2.532
setNodeFillOpacityDirect	0.708	0.000	5.047
setNodeFontSizeDirect	0.628	0.004	4.024
setNodeHeightDirect	0.696	0.008	4.037
setNodeImageDirect	0.688	0.012	4.142
setNodeLabelColorDirect	0.696	0.024	4.245
setNodeLabelDirect	0.740	0.016	4.185
setNodeLabelOpacityDirect	0.560	0.008	3.883
setNodeLabelRule	0.636	0.016	6.123
setNodeOpacityDirect	0.568	0.004	5.290
setNodeShapeDirect	0.568	0.008	5.555
setNodeShapeRule	0.372	0.000	1.515
setNodeSizeDirect	0.564	0.012	4.452
setNodeSizeRule	0.669	0.008	7.481
setNodeTooltipRule	0.632	0.004	8.568
setNodeWidthDirect	0.592	0.004	4.495
setPosition	0.632	0.000	5.923
setTooltipDismissDelay	0.708	0.008	8.014
setTooltipInitialDelay	0.740	0.000	6.061
setVisualStyle	0.832	0.020	9.247
setWindowSize	0.784	0.032	6.209
setZoom	0.740	0.032	6.098
showGraphicsDetails	0.008	0.008	0.014
unhideAll	0.860	0.040	6.445
validCyWin	0.344	0.008	0.390
version	0.008	0.000	0.012