BioC 2.9: CHECK report for RCytoscape on wilson2

Package: RCytoscape

Version: 1.3.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings RCytoscape_1.3.0.tar.gz

StartedAt: 2011-06-06 13:43:42 -0700 (Mon, 06 Jun 2011)

EndedAt: 2011-06-06 14:05:44 -0700 (Mon, 06 Jun 2011)

EllapsedTime: 1321.9 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 2.14.0 Under development (unstable) (2011-05-30 r56024)
* 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 ‘1.3.0’
* 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 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	0.076	0.004	0.109
CytoscapeConnectionClass-class	0.000	0.000	0.001
CytoscapeWindow	0.048	0.000	0.082
CytoscapeWindowClass-class	0.092	0.000	0.119
addCyEdge	0.432	0.008	4.715
addCyNode	0.296	0.004	3.569
addGraphToGraph	0.412	0.016	5.961
clearMsg	0.012	0.000	0.011
clearSelection	0.312	0.008	4.430
copyVisualStyle	0.392	0.012	5.523
createWindowFromSelection	1.620	0.032	5.329
cy2.edge.names	0.024	0.000	0.024
deleteAllWindows	0.364	0.004	1.238
deleteEdgeAttribute	0.392	0.016	3.753
deleteNodeAttribute	0.404	0.000	3.682
deleteSelectedEdges	0.444	0.020	3.796
deleteSelectedNodes	0.352	0.016	4.727
deleteWindow	0.388	0.000	3.760
displayGraph	0.308	0.000	5.573
dockPanel	0.020	0.004	0.027
eda	0.024	0.000	0.023
eda.names	0.020	0.000	0.019
existing.CytoscapeWindow	1.036	0.032	4.152
fitContent	0.356	0.008	4.769
fitSelectedContent	0.436	0.016	4.721
floatPanel	0.012	0.004	0.063
getAllEdgeAttributes	0.292	0.004	3.643
getAllEdges	0.084	0.004	0.107
getAllNodeAttributes	0.292	0.008	3.555
getAllNodes	0.096	0.000	0.119
getArrowShapes	0.012	0.000	0.012
getAttributeClassNames	0.000	0.000	0.001
getCenter	0.308	0.004	3.600
getDefaultBackgroundColor	0.012	0.000	0.012
getDefaultEdgeReverseSelectionColor	0.012	0.000	0.012
getDefaultEdgeSelectionColor	0.012	0.000	0.012
getDefaultNodeReverseSelectionColor	0.008	0.000	0.013
getDefaultNodeSelectionColor	0.012	0.000	0.012
getDirectlyModifiableVisualProperties	0.028	0.000	0.026
getEdgeAttribute	0.352	0.016	4.680
getEdgeAttributeNames	0.012	0.000	0.012
getEdgeCount	0.316	0.012	4.610
getFirstNeighbors	0.364	0.016	3.637
getGraph	0.100	0.000	0.119
getGraphFromCyWindow	1.052	0.020	4.404
getLayoutNameMapping	0.036	0.000	0.037
getLayoutNames	0.012	0.000	0.015
getLayoutPropertyNames	0.016	0.000	0.017
getLayoutPropertyType	0.100	0.000	0.106
getLayoutPropertyValue	0.096	0.000	0.106
getLineStyles	0.012	0.000	0.014
getNodeAttribute	0.352	0.000	3.602
getNodeAttributeNames	0.008	0.000	0.012
getNodeCount	0.340	0.012	4.608
getNodeShapes	0.012	0.000	0.014
getPosition	0.328	0.012	3.606
getSelectedEdgeCount	0.384	0.008	3.692
getSelectedEdges	0.352	0.012	3.621
getSelectedNodeCount	0.376	0.008	4.682
getSelectedNodes	0.393	0.012	3.673
getViewCoordinates	0.356	0.004	3.657
getVisualStyleNames	0.012	0.000	0.012
getWindowCount	0.268	0.012	0.323
getWindowID	0.428	0.004	3.498
getWindowList	0.112	0.000	0.114
getZoom	0.404	0.008	4.673
hideAllPanels	0.264	0.000	0.380
hideNodes	0.204	0.000	0.230
hidePanel	0.020	0.000	0.021
hideSelectedEdges	0.204	0.008	0.478
hideSelectedNodes	0.228	0.008	0.502
initEdgeAttribute	0.000	0.000	0.002
initNodeAttribute	0.000	0.000	0.002
invertEdgeSelection	0.168	0.000	0.200
invertNodeSelection	0.208	0.004	0.246
layout	0.400	0.004	4.724
lockNodeDimensions	0.504	0.036	3.839
makeRandomGraph	0.012	0.000	0.021
makeSimpleGraph	0.032	0.000	0.030
msg	0.008	0.000	0.012
new.CytoscapeWindow	0.140	0.000	0.172
noa	0.016	0.000	0.019
noa.names	0.016	0.000	0.019
ping	0.008	0.000	0.013
raiseWindow	0.192	0.000	0.228
redraw	0.172	0.008	0.229
saveImage	0.372	0.004	3.641
saveNetwork	0.376	0.004	4.639
selectEdges	0.472	0.004	3.799
selectFirstNeighborsOfSelectedNodes	0.560	0.016	4.866
selectNodes	0.240	0.000	0.266
sendEdges	0.208	0.000	1.234
sendNodes	0.200	0.004	0.224
setCenter	0.476	0.048	8.855
setDefaultBackgroundColor	0.008	0.004	0.013
setDefaultEdgeColor	0.408	0.024	3.700
setDefaultEdgeLineWidth	0.420	0.000	3.727
setDefaultEdgeReverseSelectionColor	0.012	0.000	0.015
setDefaultEdgeSelectionColor	0.012	0.000	0.012
setDefaultNodeBorderColor	0.412	0.020	3.740
setDefaultNodeBorderWidth	0.440	0.008	3.709
setDefaultNodeColor	0.444	0.004	3.718
setDefaultNodeFontSize	0.440	0.004	3.791
setDefaultNodeLabelColor	0.448	0.000	3.712
setDefaultNodeReverseSelectionColor	0.008	0.004	0.014
setDefaultNodeSelectionColor	0.012	0.000	0.013
setDefaultNodeShape	0.448	0.008	3.748
setDefaultNodeSize	0.440	0.012	4.733
setEdgeAttributes	0.272	0.008	2.306
setEdgeAttributesDirect	0.244	0.000	1.272
setEdgeColorDirect	0.484	0.016	3.838
setEdgeColorRule	0.320	0.008	4.294
setEdgeFontSizeDirect	1.232	0.016	4.671
setEdgeLabelColorDirect	0.556	0.008	3.920
setEdgeLabelDirect	1.148	0.016	6.517
setEdgeLabelOpacityDirect	1.205	0.028	5.572
setEdgeLabelRule	0.456	0.004	4.735
setEdgeLabelWidthDirect	1.084	0.016	4.515
setEdgeLineStyleDirect	1.140	0.024	4.508
setEdgeLineStyleRule	0.260	0.004	1.291
setEdgeLineWidthDirect	0.820	0.000	6.186
setEdgeLineWidthRule	0.452	0.012	4.769
setEdgeOpacityDirect	1.108	0.020	5.794
setEdgeSourceArrowColorDirect	0.692	0.012	10.695
setEdgeSourceArrowColorRule	0.244	0.004	1.530
setEdgeSourceArrowOpacityDirect	0.852	0.024	12.009
setEdgeSourceArrowRule	0.300	0.000	1.384
setEdgeSourceArrowShapeDirect	0.864	0.044	14.974
setEdgeTargetArrowColorDirect	0.676	0.012	11.082
setEdgeTargetArrowColorRule	0.28	0.00	1.32
setEdgeTargetArrowOpacityDirect	0.908	0.004	4.245
setEdgeTargetArrowRule	0.288	0.004	1.317
setEdgeTargetArrowShapeDirect	1.004	0.048	13.410
setEdgeTooltipDirect	0.604	0.016	4.954
setEdgeTooltipRule	0.508	0.028	5.148
setGraph	0.272	0.000	0.299
setLayoutProperties	0.052	0.004	0.061
setNodeAttributes	0.336	0.000	0.381
setNodeBorderColorRule	0.352	0.000	2.401
setNodeBorderOpacityDirect	0.492	0.008	3.805
setNodeBorderWidthRule	0.496	0.008	4.790
setNodeColorDirect	0.532	0.000	4.829
setNodeColorRule	0.361	0.000	2.394
setNodeFillOpacityDirect	0.528	0.000	4.010
setNodeFontSizeDirect	0.504	0.012	3.808
setNodeHeightDirect	0.552	0.000	4.882
setNodeImageDirect	0.568	0.012	4.921
setNodeLabelDirect	0.548	0.004	3.975
setNodeLabelOpacityDirect	0.552	0.004	3.872
setNodeLabelRule	0.712	0.008	5.033
setNodeOpacityDirect	0.564	0.008	3.861
setNodeShapeDirect	0.604	0.000	3.982
setNodeShapeRule	0.364	0.000	1.403
setNodeSizeDirect	0.588	0.008	4.899
setNodeSizeRule	0.780	0.008	8.112
setNodeTooltipRule	0.592	0.004	7.934
setNodeWidthDirect	0.580	0.012	4.063
setNotAttributesDirect	0.336	0.008	0.367
setPosition	0.560	0.000	4.908
setVisualStyle	0.696	0.008	7.611
setWindowSize	0.620	0.020	6.084
setZoom	0.596	0.028	5.939
showGraphicsDetails	0.012	0.000	0.013
unhideAll	0.608	0.032	4.005
unhideNodes	0.484	0.012	1.703
validCyWin	0.340	0.008	0.371
version	0.008	0.000	0.011

Summary

Command output