Package: RCytoscape

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RCytoscape_1.3.0.tar.gz

StartedAt: 2011-05-09 16:34:09 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 17:07:33 -0700 (Mon, 09 May 2011)

EllapsedTime: 2004.9 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) (2011-04-24 r55634)
* 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 ‘1.3.0’
* 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 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	0.197
CytoscapeConnectionClass-class	0.001	0.000	0.002
CytoscapeWindow	0.077	0.001	0.154
CytoscapeWindowClass-class	0.130	0.001	0.166
addCyEdge	0.547	0.010	6.869
addCyNode	0.440	0.011	6.738
addGraphToGraph	0.636	0.016	9.542
clearMsg	0.014	0.001	0.017
clearSelection	0.449	0.010	6.556
copyVisualStyle	0.516	0.014	7.832
createWindowFromSelection	1.798	0.041	8.659
cy2.edge.names	0.03	0.00	0.03
deleteAllWindows	0.420	0.009	1.435
deleteEdgeAttribute	0.433	0.009	6.733
deleteNodeAttribute	0.439	0.009	6.730
deleteSelectedEdges	0.483	0.010	6.800
deleteSelectedNodes	0.459	0.010	6.748
deleteWindow	0.561	0.013	6.931
displayGraph	0.400	0.008	6.706
dockPanel	0.029	0.001	0.035
eda	0.029	0.000	0.028
eda.names	0.023	0.000	0.023
existing.CytoscapeWindow	1.473	0.034	7.804
fitContent	0.478	0.010	5.829
fitSelectedContent	0.523	0.012	6.876
floatPanel	0.029	0.001	0.095
getAllEdgeAttributes	0.434	0.009	6.759
getAllEdges	0.119	0.002	0.151
getAllNodeAttributes	0.441	0.009	6.724
getAllNodes	0.145	0.003	0.172
getArrowShapes	0.017	0.000	0.019
getAttributeClassNames	0.001	0.001	0.002
getCenter	0.496	0.012	6.820
getDefaultBackgroundColor	0.015	0.001	0.017
getDefaultEdgeReverseSelectionColor	0.015	0.001	0.017
getDefaultEdgeSelectionColor	0.015	0.001	0.017
getDefaultNodeReverseSelectionColor	0.015	0.001	0.017
getDefaultNodeSelectionColor	0.017	0.001	0.019
getDirectlyModifiableVisualProperties	0.032	0.001	0.035
getEdgeAttribute	0.460	0.008	6.770
getEdgeAttributeNames	0.017	0.001	0.019
getEdgeCount	0.449	0.009	6.719
getFirstNeighbors	0.521	0.012	5.812
getGraph	0.144	0.002	0.171
getGraphFromCyWindow	1.504	0.032	7.939
getLayoutNameMapping	0.039	0.000	0.043
getLayoutNames	0.020	0.000	0.022
getLayoutPropertyNames	0.018	0.000	0.020
getLayoutPropertyType	0.136	0.003	0.149
getLayoutPropertyValue	0.136	0.003	0.150
getLineStyles	0.021	0.001	0.023
getNodeAttribute	0.477	0.010	6.779
getNodeAttributeNames	0.017	0.000	0.019
getNodeCount	0.476	0.009	6.772
getNodeShapes	0.021	0.000	0.023
getPosition	0.474	0.009	6.755
getSelectedEdgeCount	0.524	0.011	6.842
getSelectedEdges	0.486	0.010	6.771
getSelectedNodeCount	0.549	0.011	6.844
getSelectedNodes	0.556	0.011	6.870
getViewCoordinates	0.514	0.009	6.834
getVisualStyleNames	0.016	0.000	0.019
getWindowCount	0.392	0.004	0.465
getWindowID	0.597	0.011	6.794
getWindowList	0.137	0.001	0.169
getZoom	0.530	0.011	6.907
hideAllPanels	0.392	0.015	0.522
hideNodes	0.300	0.006	0.376
hidePanel	0.031	0.002	0.043
hideSelectedEdges	0.304	0.006	0.584
hideSelectedNodes	0.347	0.006	0.650
initEdgeAttribute	0.003	0.000	0.003
initNodeAttribute	0.003	0.000	0.003
invertEdgeSelection	0.253	0.003	0.294
invertNodeSelection	0.295	0.005	0.343
layout	0.523	0.008	6.856
lockNodeDimensions	0.605	0.011	7.138
makeRandomGraph	0.024	0.000	0.026
makeSimpleGraph	0.060	0.001	0.061
msg	0.015	0.000	0.063
new.CytoscapeWindow	0.205	0.003	0.410
noa	0.023	0.000	0.036
noa.names	0.026	0.001	0.038
ping	0.013	0.000	0.034
raiseWindow	0.240	0.003	0.483
redraw	0.248	0.002	0.543
saveImage	0.593	0.011	6.419
saveNetwork	0.528	0.009	7.115
selectEdges	0.625	0.011	7.446
selectFirstNeighborsOfSelectedNodes	0.752	0.015	7.832
selectNodes	0.327	0.005	0.651
sendEdges	0.292	0.003	2.572
sendNodes	0.268	0.002	0.443
setCenter	0.693	0.075	12.614
setDefaultBackgroundColor	0.017	0.003	0.041
setDefaultEdgeColor	0.602	0.020	7.421
setDefaultEdgeLineWidth	0.597	0.010	7.193
setDefaultEdgeReverseSelectionColor	0.018	0.001	0.020
setDefaultEdgeSelectionColor	0.018	0.001	0.020
setDefaultNodeBorderColor	0.616	0.012	6.908
setDefaultNodeBorderWidth	0.599	0.008	6.884
setDefaultNodeColor	0.603	0.010	6.921
setDefaultNodeFontSize	0.614	0.011	6.973
setDefaultNodeLabelColor	0.619	0.010	6.918
setDefaultNodeReverseSelectionColor	0.017	0.000	0.018
setDefaultNodeSelectionColor	0.017	0.001	0.019
setDefaultNodeShape	0.643	0.010	6.934
setDefaultNodeSize	0.620	0.009	6.903
setEdgeAttributes	0.394	0.004	4.426
setEdgeAttributesDirect	0.324	0.004	2.353
setEdgeColorDirect	0.655	0.010	7.013
setEdgeColorRule	0.472	0.007	7.389
setEdgeFontSizeDirect	1.744	0.039	7.267
setEdgeLabelColorDirect	0.769	0.012	7.184
setEdgeLabelDirect	1.616	0.040	8.143
setEdgeLabelOpacityDirect	1.583	0.034	8.093
setEdgeLabelRule	0.717	0.017	7.024
setEdgeLabelWidthDirect	1.567	0.031	8.076
setEdgeLineStyleDirect	1.692	0.041	8.240
setEdgeLineStyleRule	0.373	0.004	2.419
setEdgeLineWidthDirect	1.137	0.022	7.559
setEdgeLineWidthRule	0.671	0.010	8.977
setEdgeOpacityDirect	1.608	0.036	8.130
setEdgeSourceArrowColorDirect	0.963	0.017	15.320
setEdgeSourceArrowColorRule	0.389	0.003	1.422
setEdgeSourceArrowOpacityDirect	1.302	0.028	14.791
setEdgeSourceArrowRule	0.409	0.005	2.442
setEdgeSourceArrowShapeDirect	1.366	0.028	16.800
setEdgeTargetArrowColorDirect	1.003	0.018	15.434
setEdgeTargetArrowColorRule	0.410	0.003	2.523
setEdgeTargetArrowOpacityDirect	1.315	0.027	7.781
setEdgeTargetArrowRule	0.439	0.005	2.494
setEdgeTargetArrowShapeDirect	1.379	0.028	16.851
setEdgeTooltipDirect	0.903	0.015	8.245
setEdgeTooltipRule	0.804	0.011	9.202
setGraph	0.403	0.002	0.432
setLayoutProperties	0.082	0.002	0.094
setNodeAttributes	0.510	0.004	0.542
setNodeBorderColorRule	0.512	0.005	4.554
setNodeBorderOpacityDirect	0.735	0.009	7.049
setNodeBorderWidthRule	0.764	0.009	9.067
setNodeColorDirect	0.763	0.009	7.069
setNodeColorRule	0.531	0.005	4.572
setNodeFillOpacityDirect	0.755	0.009	7.190
setNodeFontSizeDirect	0.770	0.010	7.108
setNodeHeightDirect	0.786	0.011	7.098
setNodeImageDirect	0.822	0.011	7.179
setNodeLabelDirect	0.786	0.010	7.273
setNodeLabelOpacityDirect	0.784	0.011	7.125
setNodeLabelRule	0.964	0.017	6.345
setNodeOpacityDirect	0.835	0.012	7.139
setNodeShapeDirect	0.817	0.011	7.215
setNodeShapeRule	0.520	0.005	2.558
setNodeSizeDirect	0.801	0.011	7.112
setNodeSizeRule	0.943	0.015	13.282
setNodeTooltipRule	0.866	0.010	13.184
setNodeWidthDirect	0.894	0.012	7.402
setNotAttributesDirect	0.511	0.004	0.553
setPosition	0.805	0.010	9.114
setVisualStyle	1.011	0.017	11.009
setWindowSize	0.914	0.053	9.424
setZoom	0.856	0.052	9.226
showGraphicsDetails	0.017	0.002	0.022
unhideAll	0.898	0.022	7.280
unhideNodes	0.626	0.022	1.705
validCyWin	0.505	0.017	0.562
version	0.014	0.001	0.016