Package: RCytoscape

Version: 1.4.4

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RCytoscape_1.4.4.tar.gz

StartedAt: 2012-03-24 03:36:11 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 04:13:57 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 2266.4 seconds

RetCode: 0

Status:  OK

CheckDir: RCytoscape.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/RCytoscape.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.4.4'
* 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 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'
 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	0.055	0.002	0.064
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.065	0.002	0.087
CytoscapeWindowClass-class	0.106	0.002	0.181
addCyEdge	0.485	0.010	6.920
addCyNode	0.435	0.008	6.773
addGraphToGraph	0.642	0.014	9.471
clearMsg	0.012	0.000	0.015
clearSelection	0.457	0.009	6.528
copyVisualStyle	0.532	0.011	6.602
createWindowFromSelection	3.730	0.098	10.886
cy2.edge.names	0.026	0.000	0.027
deleteAllWindows	0.393	0.009	0.752
deleteEdgeAttribute	0.435	0.010	7.233
deleteNodeAttribute	0.435	0.010	6.509
deleteSelectedEdges	0.472	0.012	6.891
deleteSelectedNodes	0.461	0.010	6.828
deleteWindow	0.535	0.011	6.944
demoSimpleGraph	0.634	0.019	12.439
displayGraph	0.412	0.009	6.834
dockPanel	0.026	0.001	0.032
eda	0.026	0.001	0.027
eda.names	0.02	0.00	0.02
existing.CytoscapeWindow	3.562	0.084	10.009
fitContent	0.448	0.010	6.817
fitSelectedContent	0.499	0.012	6.918
floatPanel	0.027	0.001	0.080
getAllEdgeAttributes	0.418	0.008	6.965
getAllEdges	0.110	0.002	0.135
getAllNodeAttributes	0.423	0.008	6.768
getAllNodes	0.133	0.003	0.160
getArrowShapes	0.015	0.000	0.017
getAttributeClassNames	0.001	0.000	0.001
getCenter	0.437	0.009	6.785
getDefaultBackgroundColor	0.014	0.001	0.018
getDefaultEdgeReverseSelectionColor	0.017	0.001	0.020
getDefaultEdgeSelectionColor	0.016	0.001	0.019
getDefaultNodeReverseSelectionColor	0.014	0.001	0.017
getDefaultNodeSelectionColor	0.013	0.001	0.016
getDirectlyModifiableVisualProperties	0.032	0.001	0.036
getEdgeAttribute	0.460	0.009	6.816
getEdgeAttributeNames	0.021	0.001	0.023
getEdgeCount	0.445	0.009	6.933
getFirstNeighbors	0.531	0.012	6.893
getGraph	0.141	0.002	0.162
getGraphFromCyWindow	3.538	0.080	10.226
getLayoutNameMapping	0.039	0.001	0.041
getLayoutNames	0.019	0.001	0.022
getLayoutPropertyNames	0.022	0.000	0.024
getLayoutPropertyType	0.152	0.005	0.182
getLayoutPropertyValue	0.138	0.004	0.165
getLineStyles	0.017	0.001	0.020
getNodeAttribute	0.482	0.009	6.892
getNodeAttributeNames	0.022	0.001	0.025
getNodeCount	0.496	0.011	7.162
getNodeShapes	0.018	0.000	0.023
getPosition	0.478	0.009	6.905
getSelectedEdgeCount	0.530	0.011	6.906
getSelectedEdges	0.507	0.010	6.853
getSelectedNodeCount	0.575	0.011	7.123
getSelectedNodes	0.584	0.012	6.979
getViewCoordinates	0.524	0.010	6.882
getVisualStyleNames	0.016	0.001	0.018
getWindowCount	0.397	0.006	0.449
getWindowID	0.654	0.012	6.725
getWindowList	0.140	0.002	0.147
getZoom	0.496	0.010	6.846
hideAllPanels	0.333	0.011	0.413
hideNodes	0.279	0.005	0.347
hidePanel	0.030	0.002	0.034
hideSelectedEdges	0.270	0.005	0.956
hideSelectedNodes	0.282	0.006	0.344
initEdgeAttribute	0.005	0.000	0.005
initNodeAttribute	0.002	0.000	0.003
invertEdgeSelection	0.232	0.004	0.258
invertNodeSelection	0.280	0.005	0.331
layout	0.517	0.009	6.882
lockNodeDimensions	0.577	0.011	7.706
makeRandomGraph	0.025	0.000	0.025
makeSimpleGraph	0.027	0.000	0.028
msg	0.015	0.000	0.062
new.CytoscapeWindow	0.196	0.002	0.429
noa	0.02	0.00	0.02
noa.names	0.02	0.00	0.02
ping	0.012	0.001	0.055
raiseWindow	0.232	0.003	0.502
redraw	0.233	0.004	0.512
restoreLayout	0.668	0.014	10.188
saveImage	0.551	0.009	6.908
saveLayout	0.676	0.012	9.347
saveNetwork	0.544	0.009	7.139
selectEdges	0.682	0.013	7.047
selectFirstNeighborsOfSelectedNodes	0.768	0.016	7.150
selectNodes	0.348	0.006	0.395
sendEdges	0.305	0.003	2.379
sendNodes	0.293	0.003	0.326
setCenter	0.790	0.120	12.293
setDefaultBackgroundColor	0.019	0.003	0.032
setDefaultEdgeColor	0.625	0.024	7.249
setDefaultEdgeLineWidth	0.622	0.010	6.978
setDefaultEdgeReverseSelectionColor	0.015	0.001	0.017
setDefaultEdgeSelectionColor	0.017	0.001	0.019
setDefaultNodeBorderColor	0.635	0.010	6.995
setDefaultNodeBorderWidth	0.618	0.010	6.990
setDefaultNodeColor	0.689	0.012	7.177
setDefaultNodeFontSize	0.652	0.011	7.079
setDefaultNodeLabelColor	0.669	0.011	7.060
setDefaultNodeReverseSelectionColor	0.016	0.001	0.019
setDefaultNodeSelectionColor	0.016	0.001	0.017
setDefaultNodeShape	0.664	0.012	7.106
setDefaultNodeSize	0.734	0.020	7.214
setEdgeAttributes	0.375	0.004	4.407
setEdgeAttributesDirect	0.316	0.003	2.353
setEdgeColorDirect	0.650	0.010	7.003
setEdgeColorRule	0.459	0.007	6.505
setEdgeFontSizeDirect	1.698	0.036	8.206
setEdgeLabelColorDirect	0.763	0.013	7.130
setEdgeLabelDirect	1.548	0.034	8.290
setEdgeLabelOpacityDirect	1.546	0.033	8.042
setEdgeLabelRule	0.647	0.010	7.002
setEdgeLabelWidthDirect	1.640	0.041	8.249
setEdgeLineStyleDirect	1.709	0.037	7.486
setEdgeLineStyleRule	0.399	0.007	2.486
setEdgeLineWidthDirect	1.153	0.021	7.634
setEdgeLineWidthRule	0.686	0.009	9.050
setEdgeOpacityDirect	1.442	0.030	48.076
setEdgeSourceArrowColorDirect	0.986	0.018	16.332
setEdgeSourceArrowColorRule	0.393	0.004	2.682
setEdgeSourceArrowOpacityDirect	1.305	0.026	15.808
setEdgeSourceArrowRule	0.394	0.004	2.628
setEdgeSourceArrowShapeDirect	1.294	0.027	17.464
setEdgeTargetArrowColorDirect	0.972	0.019	15.438
setEdgeTargetArrowColorRule	0.421	0.004	2.463
setEdgeTargetArrowOpacityDirect	1.296	0.024	7.911
setEdgeTargetArrowRule	0.416	0.003	2.447
setEdgeTargetArrowShapeDirect	1.338	0.026	16.807
setEdgeTooltipDirect	0.890	0.014	8.281
setEdgeTooltipRule	0.744	0.010	9.124
setGraph	0.406	0.004	0.442
setLayoutProperties	0.084	0.002	0.096
setNodeAttributes	0.518	0.005	0.589
setNodeAttributesDirect	0.440	0.004	0.471
setNodeBorderColorDirect	0.797	0.011	7.452
setNodeBorderColorRule	0.519	0.005	4.561
setNodeBorderOpacityDirect	0.759	0.009	7.158
setNodeBorderWidthDirect	0.815	0.010	6.210
setNodeBorderWidthRule	0.797	0.010	9.165
setNodeColorDirect	0.839	0.010	7.629
setNodeColorRule	0.605	0.009	4.707
setNodeFillOpacityDirect	0.737	0.011	7.415
setNodeFontSizeDirect	0.754	0.011	7.157
setNodeHeightDirect	0.775	0.010	7.148
setNodeImageDirect	0.799	0.011	7.377
setNodeLabelColorDirect	0.785	0.010	7.180
setNodeLabelDirect	0.767	0.010	7.183
setNodeLabelOpacityDirect	0.788	0.010	7.155
setNodeLabelRule	0.922	0.017	7.693
setNodeOpacityDirect	0.799	0.011	9.173
setNodeShapeDirect	0.805	0.010	7.213
setNodeShapeRule	0.529	0.005	2.572
setNodeSizeDirect	0.812	0.011	6.900
setNodeSizeRule	0.990	0.016	13.433
setNodeTooltipRule	0.917	0.013	13.363
setNodeWidthDirect	0.886	0.013	7.331
setPosition	0.826	0.010	9.357
setTooltipDismissDelay	0.919	0.013	10.318
setTooltipInitialDelay	0.947	0.014	11.381
setVisualStyle	1.126	0.019	10.523
setWindowSize	0.952	0.055	9.862
setZoom	0.995	0.069	8.464
showGraphicsDetails	0.020	0.006	0.028
unhideAll	0.920	0.048	9.392
validCyWin	0.497	0.022	0.546
version	0.013	0.001	0.016