Package: RCytoscape

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RCytoscape_1.3.2.tar.gz

StartedAt: 2011-06-22 04:53:34 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 05:26:52 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 1997.4 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 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘1.3.2’
* 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 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
** 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	0.112	0.004	0.144
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.073	0.001	0.107
CytoscapeWindowClass-class	0.126	0.001	0.165
addCyEdge	0.551	0.011	6.906
addCyNode	0.446	0.011	6.933
addGraphToGraph	0.629	0.016	9.375
clearMsg	0.015	0.000	0.028
clearSelection	0.453	0.011	6.615
copyVisualStyle	0.499	0.012	7.644
createWindowFromSelection	1.891	0.050	8.645
cy2.edge.names	0.032	0.000	0.040
deleteAllWindows	0.434	0.012	1.464
deleteEdgeAttribute	0.455	0.012	6.755
deleteNodeAttribute	0.476	0.012	6.778
deleteSelectedEdges	0.485	0.012	6.827
deleteSelectedNodes	0.459	0.011	6.753
deleteWindow	0.561	0.014	6.896
displayGraph	0.408	0.009	6.682
dockPanel	0.028	0.001	0.035
eda	0.025	0.000	0.026
eda.names	0.025	0.001	0.026
existing.CytoscapeWindow	1.454	0.033	7.638
fitContent	0.477	0.011	6.801
fitSelectedContent	0.564	0.014	6.859
floatPanel	0.030	0.001	0.106
getAllEdgeAttributes	0.417	0.009	6.684
getAllEdges	0.117	0.002	0.141
getAllNodeAttributes	0.421	0.010	6.687
getAllNodes	0.137	0.003	0.167
getArrowShapes	0.016	0.001	0.019
getAttributeClassNames	0.001	0.000	0.001
getCenter	0.444	0.010	6.756
getDefaultBackgroundColor	0.016	0.001	0.018
getDefaultEdgeReverseSelectionColor	0.015	0.001	0.016
getDefaultEdgeSelectionColor	0.015	0.001	0.017
getDefaultNodeReverseSelectionColor	0.015	0.001	0.018
getDefaultNodeSelectionColor	0.017	0.001	0.020
getDirectlyModifiableVisualProperties	0.033	0.001	0.043
getEdgeAttribute	0.473	0.010	6.774
getEdgeAttributeNames	0.016	0.001	0.020
getEdgeCount	0.450	0.009	6.727
getFirstNeighbors	0.506	0.010	6.798
getGraph	0.143	0.002	0.164
getGraphFromCyWindow	1.481	0.029	7.890
getLayoutNameMapping	0.040	0.001	0.043
getLayoutNames	0.023	0.001	0.024
getLayoutPropertyNames	0.018	0.001	0.019
getLayoutPropertyType	0.141	0.004	0.156
getLayoutPropertyValue	0.149	0.005	0.166
getLineStyles	0.019	0.001	0.021
getNodeAttribute	0.458	0.008	6.741
getNodeAttributeNames	0.017	0.000	0.020
getNodeCount	0.470	0.009	6.753
getNodeShapes	0.018	0.001	0.020
getPosition	0.459	0.009	6.740
getSelectedEdgeCount	0.532	0.011	6.888
getSelectedEdges	0.479	0.009	6.769
getSelectedNodeCount	0.534	0.010	6.896
getSelectedNodes	0.555	0.011	6.845
getViewCoordinates	0.512	0.010	6.871
getVisualStyleNames	0.018	0.001	0.020
getWindowCount	0.395	0.006	0.456
getWindowID	0.592	0.010	6.649
getWindowList	0.141	0.002	0.146
getZoom	0.512	0.010	6.798
hideAllPanels	0.361	0.011	0.581
hideNodes	0.276	0.004	0.317
hidePanel	0.027	0.001	0.030
hideSelectedEdges	0.303	0.006	0.598
hideSelectedNodes	0.349	0.007	0.653
initEdgeAttribute	0.004	0.000	0.003
initNodeAttribute	0.003	0.000	0.003
invertEdgeSelection	0.246	0.003	0.286
invertNodeSelection	0.296	0.005	0.339
layout	0.515	0.010	6.853
lockNodeDimensions	0.682	0.017	6.989
makeRandomGraph	0.027	0.001	0.029
makeSimpleGraph	0.059	0.002	0.061
msg	0.015	0.000	0.023
new.CytoscapeWindow	0.221	0.002	0.249
noa	0.025	0.000	0.026
noa.names	0.024	0.000	0.024
ping	0.015	0.001	0.017
raiseWindow	0.246	0.003	0.275
redraw	0.243	0.003	0.283
saveImage	0.524	0.008	6.811
saveNetwork	0.544	0.009	6.832
selectEdges	0.649	0.013	7.113
selectFirstNeighborsOfSelectedNodes	0.773	0.018	7.201
selectNodes	0.342	0.006	0.394
sendEdges	0.298	0.005	2.339
sendNodes	0.273	0.004	0.330
setCenter	0.717	0.075	12.119
setDefaultBackgroundColor	0.025	0.007	0.034
setDefaultEdgeColor	0.618	0.019	6.935
setDefaultEdgeLineWidth	0.597	0.010	6.949
setDefaultEdgeReverseSelectionColor	0.016	0.001	0.018
setDefaultEdgeSelectionColor	0.018	0.001	0.020
setDefaultNodeBorderColor	0.605	0.011	6.903
setDefaultNodeBorderWidth	0.606	0.011	6.902
setDefaultNodeColor	0.612	0.011	6.939
setDefaultNodeFontSize	0.623	0.012	7.063
setDefaultNodeLabelColor	0.614	0.010	7.102
setDefaultNodeReverseSelectionColor	0.016	0.000	0.022
setDefaultNodeSelectionColor	0.016	0.000	0.049
setDefaultNodeShape	0.637	0.011	7.399
setDefaultNodeSize	0.619	0.010	7.448
setEdgeAttributes	0.390	0.004	4.716
setEdgeAttributesDirect	0.328	0.003	2.629
setEdgeColorDirect	0.648	0.010	7.815
setEdgeColorRule	0.461	0.007	7.494
setEdgeFontSizeDirect	1.734	0.040	10.140
setEdgeLabelColorDirect	0.792	0.014	7.559
setEdgeLabelDirect	1.581	0.032	8.115
setEdgeLabelOpacityDirect	1.610	0.042	8.061
setEdgeLabelRule	0.635	0.011	6.940
setEdgeLabelWidthDirect	1.553	0.034	7.131
setEdgeLineStyleDirect	1.672	0.037	8.304
setEdgeLineStyleRule	0.373	0.004	2.412
setEdgeLineWidthDirect	1.139	0.023	7.533
setEdgeLineWidthRule	0.668	0.011	8.974
setEdgeOpacityDirect	1.591	0.035	7.206
setEdgeSourceArrowColorDirect	0.956	0.017	15.295
setEdgeSourceArrowColorRule	0.389	0.003	2.421
setEdgeSourceArrowOpacityDirect	1.276	0.025	14.739
setEdgeSourceArrowRule	0.421	0.006	2.464
setEdgeSourceArrowShapeDirect	1.332	0.026	16.736
setEdgeTargetArrowColorDirect	0.995	0.019	15.562
setEdgeTargetArrowColorRule	0.415	0.005	2.482
setEdgeTargetArrowOpacityDirect	1.308	0.026	7.772
setEdgeTargetArrowRule	0.433	0.005	2.545
setEdgeTargetArrowShapeDirect	1.438	0.031	16.862
setEdgeTooltipDirect	0.876	0.014	8.245
setEdgeTooltipRule	0.709	0.009	9.115
setGraph	0.408	0.004	0.468
setLayoutProperties	0.083	0.002	0.120
setNodeAttributes	0.510	0.006	0.752
setNodeBorderColorRule	0.502	0.005	4.547
setNodeBorderOpacityDirect	0.739	0.011	7.058
setNodeBorderWidthRule	0.744	0.010	9.051
setNodeColorDirect	0.758	0.011	7.077
setNodeColorRule	0.533	0.006	4.573
setNodeFillOpacityDirect	0.772	0.011	7.193
setNodeFontSizeDirect	0.761	0.011	7.075
setNodeHeightDirect	0.776	0.011	7.084
setNodeImageDirect	0.828	0.012	7.434
setNodeLabelDirect	0.778	0.010	6.208
setNodeLabelOpacityDirect	0.781	0.010	7.107
setNodeLabelRule	0.961	0.018	7.404
setNodeOpacityDirect	0.843	0.013	7.167
setNodeShapeDirect	0.807	0.010	7.293
setNodeShapeRule	0.534	0.007	2.602
setNodeSizeDirect	0.801	0.011	7.186
setNodeSizeRule	0.988	0.014	13.313
setNodeTooltipRule	0.860	0.012	13.187
setNodeWidthDirect	0.815	0.010	7.249
setNotAttributesDirect	0.500	0.003	0.533
setPosition	0.805	0.009	9.106
setVisualStyle	1.006	0.017	10.990
setWindowSize	0.915	0.050	9.431
setZoom	0.864	0.053	9.222
showGraphicsDetails	0.018	0.002	0.021
unhideAll	0.889	0.026	7.252
unhideNodes	0.625	0.023	1.695
validCyWin	0.498	0.016	0.555
version	0.014	0.000	0.016