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: 2011-07-07 05:16:17 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:49:40 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 2003.0 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) (2011-06-22 r56208)
* 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 '1.3.2'
* 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	0.105	0.004	0.282
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.072	0.001	0.176
CytoscapeWindowClass-class	0.129	0.003	0.268
addCyEdge	0.527	0.013	6.968
addCyNode	0.430	0.010	6.824
addGraphToGraph	0.616	0.015	8.425
clearMsg	0.012	0.001	0.021
clearSelection	0.442	0.011	6.608
copyVisualStyle	0.491	0.012	7.665
createWindowFromSelection	1.743	0.041	8.536
cy2.edge.names	0.029	0.000	0.033
deleteAllWindows	0.409	0.010	1.413
deleteEdgeAttribute	0.440	0.013	6.878
deleteNodeAttribute	0.432	0.011	6.746
deleteSelectedEdges	0.462	0.011	6.834
deleteSelectedNodes	0.461	0.011	6.793
deleteWindow	0.548	0.013	6.925
displayGraph	0.400	0.009	6.686
dockPanel	0.026	0.001	0.038
eda	0.028	0.000	0.029
eda.names	0.024	0.000	0.024
existing.CytoscapeWindow	1.440	0.035	7.630
fitContent	0.447	0.011	6.771
fitSelectedContent	0.501	0.013	6.953
floatPanel	0.027	0.001	0.071
getAllEdgeAttributes	0.415	0.009	5.743
getAllEdges	0.116	0.003	0.158
getAllNodeAttributes	0.413	0.009	6.696
getAllNodes	0.143	0.003	0.174
getArrowShapes	0.015	0.001	0.017
getAttributeClassNames	0.001	0.000	0.001
getCenter	0.435	0.009	6.752
getDefaultBackgroundColor	0.013	0.000	0.016
getDefaultEdgeReverseSelectionColor	0.016	0.000	0.022
getDefaultEdgeSelectionColor	0.014	0.000	0.015
getDefaultNodeReverseSelectionColor	0.014	0.000	0.015
getDefaultNodeSelectionColor	0.014	0.001	0.016
getDirectlyModifiableVisualProperties	0.030	0.001	0.033
getEdgeAttribute	0.448	0.008	6.728
getEdgeAttributeNames	0.015	0.001	0.017
getEdgeCount	0.442	0.010	6.759
getFirstNeighbors	0.501	0.010	6.786
getGraph	0.145	0.002	0.172
getGraphFromCyWindow	1.460	0.034	7.868
getLayoutNameMapping	0.041	0.001	0.044
getLayoutNames	0.019	0.001	0.026
getLayoutPropertyNames	0.020	0.001	0.023
getLayoutPropertyType	0.135	0.004	0.152
getLayoutPropertyValue	0.133	0.004	0.150
getLineStyles	0.017	0.001	0.019
getNodeAttribute	0.470	0.010	6.761
getNodeAttributeNames	0.016	0.000	0.018
getNodeCount	0.462	0.009	6.735
getNodeShapes	0.016	0.001	0.019
getPosition	0.476	0.011	6.788
getSelectedEdgeCount	0.514	0.011	6.848
getSelectedEdges	0.493	0.009	6.798
getSelectedNodeCount	0.548	0.012	6.838
getSelectedNodes	0.575	0.012	6.869
getViewCoordinates	0.515	0.011	6.835
getVisualStyleNames	0.016	0.001	0.018
getWindowCount	0.399	0.005	0.472
getWindowID	0.595	0.009	6.652
getWindowList	0.144	0.002	0.154
getZoom	0.564	0.010	6.847
hideAllPanels	0.364	0.016	0.488
hideNodes	0.289	0.006	0.383
hidePanel	0.028	0.001	0.031
hideSelectedEdges	0.288	0.005	0.595
hideSelectedNodes	0.323	0.005	0.610
initEdgeAttribute	0.003	0.000	0.004
initNodeAttribute	0.003	0.000	0.003
invertEdgeSelection	0.240	0.003	0.299
invertNodeSelection	0.277	0.003	0.312
layout	0.522	0.010	6.854
lockNodeDimensions	0.590	0.012	6.900
makeRandomGraph	0.023	0.001	0.025
makeSimpleGraph	0.033	0.001	0.035
msg	0.014	0.000	0.016
new.CytoscapeWindow	0.214	0.003	0.246
noa	0.023	0.001	0.023
noa.names	0.024	0.000	0.025
ping	0.013	0.001	0.016
raiseWindow	0.256	0.003	0.280
redraw	0.258	0.003	0.286
saveImage	0.532	0.010	5.832
saveNetwork	0.538	0.010	6.864
selectEdges	0.649	0.014	7.030
selectFirstNeighborsOfSelectedNodes	0.754	0.017	7.100
selectNodes	0.327	0.004	0.364
sendEdges	0.295	0.003	2.325
sendNodes	0.285	0.003	0.330
setCenter	0.706	0.080	12.369
setDefaultBackgroundColor	0.018	0.003	0.022
setDefaultEdgeColor	0.598	0.019	6.924
setDefaultEdgeLineWidth	0.617	0.011	6.923
setDefaultEdgeReverseSelectionColor	0.015	0.000	0.018
setDefaultEdgeSelectionColor	0.015	0.000	0.018
setDefaultNodeBorderColor	0.608	0.013	6.927
setDefaultNodeBorderWidth	0.618	0.011	6.932
setDefaultNodeColor	0.615	0.010	7.042
setDefaultNodeFontSize	0.615	0.010	7.033
setDefaultNodeLabelColor	0.618	0.012	7.414
setDefaultNodeReverseSelectionColor	0.016	0.001	0.026
setDefaultNodeSelectionColor	0.015	0.000	0.032
setDefaultNodeShape	0.648	0.011	7.346
setDefaultNodeSize	0.627	0.011	7.540
setEdgeAttributes	0.395	0.005	4.728
setEdgeAttributesDirect	0.348	0.003	2.428
setEdgeColorDirect	0.654	0.011	7.492
setEdgeColorRule	0.517	0.013	7.597
setEdgeFontSizeDirect	1.675	0.042	9.894
setEdgeLabelColorDirect	0.761	0.014	7.468
setEdgeLabelDirect	1.524	0.035	8.000
setEdgeLabelOpacityDirect	1.517	0.034	7.950
setEdgeLabelRule	0.633	0.009	6.962
setEdgeLabelWidthDirect	1.507	0.033	8.073
setEdgeLineStyleDirect	1.644	0.040	8.084
setEdgeLineStyleRule	0.412	0.006	2.455
setEdgeLineWidthDirect	1.144	0.022	7.514
setEdgeLineWidthRule	0.683	0.010	9.000
setEdgeOpacityDirect	1.537	0.032	8.071
setEdgeSourceArrowColorDirect	0.967	0.018	15.316
setEdgeSourceArrowColorRule	0.397	0.004	2.430
setEdgeSourceArrowOpacityDirect	1.247	0.025	14.666
setEdgeSourceArrowRule	0.463	0.007	2.508
setEdgeSourceArrowShapeDirect	1.298	0.030	16.702
setEdgeTargetArrowColorDirect	0.981	0.019	15.447
setEdgeTargetArrowColorRule	0.396	0.003	2.437
setEdgeTargetArrowOpacityDirect	1.265	0.025	7.661
setEdgeTargetArrowRule	0.432	0.004	2.466
setEdgeTargetArrowShapeDirect	1.324	0.029	16.730
setEdgeTooltipDirect	0.864	0.014	8.197
setEdgeTooltipRule	0.714	0.009	9.123
setGraph	0.432	0.007	0.571
setLayoutProperties	0.080	0.003	0.198
setNodeAttributes	0.510	0.006	0.566
setNodeBorderColorRule	0.528	0.007	4.583
setNodeBorderOpacityDirect	0.744	0.010	7.062
setNodeBorderWidthRule	0.756	0.011	9.142
setNodeColorDirect	0.776	0.012	7.136
setNodeColorRule	0.552	0.007	4.621
setNodeFillOpacityDirect	0.763	0.012	7.225
setNodeFontSizeDirect	0.775	0.011	7.082
setNodeHeightDirect	0.805	0.013	7.145
setNodeImageDirect	0.814	0.012	7.195
setNodeLabelDirect	0.805	0.012	6.311
setNodeLabelOpacityDirect	0.791	0.013	7.140
setNodeLabelRule	0.960	0.016	7.314
setNodeOpacityDirect	0.880	0.012	7.195
setNodeShapeDirect	0.795	0.010	7.204
setNodeShapeRule	0.521	0.005	2.560
setNodeSizeDirect	0.793	0.011	7.102
setNodeSizeRule	0.922	0.013	13.262
setNodeTooltipRule	0.871	0.013	13.213
setNodeWidthDirect	0.829	0.013	7.251
setNotAttributesDirect	0.514	0.004	0.553
setPosition	0.843	0.011	8.150
setVisualStyle	0.999	0.017	9.705
setWindowSize	0.909	0.050	9.431
setZoom	0.882	0.058	9.311
showGraphicsDetails	0.016	0.003	0.020
unhideAll	0.922	0.030	7.387
unhideNodes	0.644	0.029	1.927
validCyWin	0.514	0.015	0.622
version	0.014	0.001	0.017