Package: RCytoscape

Version: 1.1.46

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RCytoscape_1.1.46.tar.gz

StartedAt: 2011-02-24 20:58:53 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:20:27 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 1293.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RCytoscape.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/RCytoscape.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.1.46’
* 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 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 ... WARNING
Subdirectory 'data' contains no data sets.
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘RCytoscape_unit_tests.R’
 OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/Users/biocbuild/bbs-2.8-bioc/meat/RCytoscape.Rcheck/00check.log’
for details

* installing *source* package ‘RCytoscape’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RCytoscape)

name	user	system	elapsed
CytoscapeConnection	0.153	0.004	0.194
CytoscapeConnectionClass-class	0.001	0.000	0.002
CytoscapeWindow	0.072	0.004	0.104
CytoscapeWindowClass-class	0.122	0.002	0.173
addCyEdge	0.503	0.013	5.810
addCyNode	0.404	0.009	6.682
addGraphToGraph	0.580	0.014	9.209
clearMsg	0.013	0.001	0.016
clearSelection	0.404	0.010	6.590
copyVisualStyle	0.479	0.016	6.397
cy.sfn	0.508	0.012	6.800
cy2.edge.names	0.026	0.001	0.027
deleteEdgeAttribute	0.445	0.010	6.747
deleteNodeAttribute	0.432	0.009	6.701
destroyAllWindows	0.201	0.005	0.564
destroyWindow	0.116	0.003	0.173
displayGraph	0.333	0.007	6.594
dockPanel	0.028	0.000	0.035
eda	0.029	0.000	0.028
eda.names	0.024	0.001	0.024
existing.CytoscapeWindow	1.335	0.032	7.660
firstNeighbors	0.089	0.002	0.135
floatPanel	0.028	0.001	0.073
getAllEdgeAttributes	0.383	0.008	6.672
getAllEdges	0.110	0.003	0.159
getAllNodeAttributes	0.395	0.009	6.693
getAllNodes	0.118	0.002	0.155
getArrowShapes	0.017	0.000	0.019
getAttributeClassNames	0.002	0.001	0.002
getDefaultBackgroundColor	0.015	0.000	0.016
getDefaultEdgeReverseSelectionColor	0.015	0.000	0.017
getDefaultEdgeSelectionColor	0.017	0.000	0.019
getDefaultNodeReverseSelectionColor	0.015	0.000	0.018
getDefaultNodeSelectionColor	0.017	0.001	0.019
getDirectlyModifiableVisualProperties	0.028	0.001	0.030
getEdgeAttribute	0.428	0.010	6.716
getEdgeAttributeNames	0.018	0.000	0.021
getEdgeCount	0.430	0.010	6.769
getGraph	0.122	0.002	0.174
getGraphFromCyWindow	1.392	0.029	7.820
getLayoutNames	0.023	0.001	0.027
getLineStyles	0.019	0.001	0.023
getNodeAttribute	0.414	0.009	6.713
getNodeAttributeNames	0.020	0.001	0.024
getNodeCount	0.418	0.009	6.698
getNodeShapes	0.022	0.001	0.024
getPosition	0.413	0.008	6.672
getSelectedEdgeCount	0.467	0.010	6.739
getSelectedEdges	0.444	0.011	6.857
getSelectedNodeCount	0.467	0.009	6.756
getSelectedNodes	0.538	0.013	6.827
getVisualStyleNames	0.016	0.001	0.019
getWindowCount	0.330	0.005	0.415
getWindowID	0.498	0.009	6.630
getWindowList	0.112	0.001	0.125
hideAllPanels	0.340	0.009	0.738
hideNodes	0.236	0.004	0.281
hidePanel	0.029	0.001	0.032
hideSelectedEdges	0.253	0.005	0.822
hideSelectedNodes	0.291	0.006	0.561
initEdgeAttribute	0.003	0.000	0.004
initNodeAttribute	0.004	0.000	0.004
invertEdgeSelection	0.219	0.003	0.262
invertNodeSelection	0.250	0.004	0.302
layout	0.454	0.009	6.727
lockNodeDimensions	0.534	0.011	6.883
makeRandomGraph	0.026	0.000	0.027
makeSimpleGraph	0.063	0.001	0.064
msg	0.015	0.001	0.017
new.CytoscapeWindow	0.177	0.002	0.212
noa	0.028	0.000	0.029
noa.names	0.027	0.000	0.026
ping	0.015	0.001	0.020
raiseWindow	0.223	0.004	0.276
redraw	0.227	0.004	0.267
removeSelectedEdges	0.272	0.004	0.313
removeSelectedNodes	0.270	0.004	0.318
resizeWindow	0.498	0.010	6.777
saveImage	0.500	0.010	6.779
selectEdge	0.574	0.012	6.885
selectEdges	0.590	0.012	6.939
selectNodes	0.310	0.004	0.351
sendEdgeAttributes	0.316	0.004	4.359
sendEdgeAttributesDirect	0.263	0.002	2.301
sendEdges	0.282	0.003	2.328
sendNodeAttributes	0.330	0.004	0.364
sendNodeAttributesDirect	0.267	0.002	0.297
sendNodes	0.273	0.003	0.312
setDefaultBackgroundColor	0.015	0.000	0.017
setDefaultEdgeColor	0.577	0.011	6.983
setDefaultEdgeLineWidth	0.572	0.010	6.842
setDefaultEdgeReverseSelectionColor	0.018	0.001	0.021
setDefaultEdgeSelectionColor	0.019	0.001	0.024
setDefaultNodeBorderColor	0.605	0.013	6.880
setDefaultNodeBorderWidth	0.593	0.011	6.926
setDefaultNodeColor	0.590	0.011	6.932
setDefaultNodeFontSize	0.590	0.011	6.867
setDefaultNodeLabelColor	0.597	0.011	6.863
setDefaultNodeReverseSelectionColor	0.016	0.000	0.017
setDefaultNodeSelectionColor	0.019	0.001	0.021
setDefaultNodeShape	0.613	0.011	6.993
setDefaultNodeSize	0.661	0.013	6.936
setEdgeColorRule	0.452	0.008	6.766
setEdgeLabelRule	0.619	0.011	6.944
setEdgeLineStyleRule	0.329	0.003	2.361
setEdgeLineWidthRule	0.597	0.011	8.876
setEdgeSourceArrowColorRule	0.337	0.004	2.376
setEdgeSourceArrowRule	0.351	0.004	2.391
setEdgeTargetArrowColorRule	0.340	0.004	2.372
setEdgeTargetArrowRule	0.351	0.004	2.391
setEdgeTooltipRule	0.626	0.011	8.989
setGraph	0.342	0.004	0.373
setNodeBorderColorRule	0.425	0.005	4.469
setNodeBorderOpacityDirect	0.631	0.011	6.917
setNodeBorderWidthRule	0.638	0.010	8.909
setNodeColorDirect	0.653	0.010	7.244
setNodeColorRule	0.448	0.004	4.496
setNodeFillOpacityDirect	0.645	0.011	6.984
setNodeHeightDirect	0.667	0.011	6.016
setNodeLabelOpacityDirect	0.652	0.009	7.200
setNodeLabelRule	0.825	0.015	7.694
setNodeOpacityDirect	0.698	0.011	7.579
setNodeShapeDirect	0.687	0.011	7.588
setNodeShapeRule	0.435	0.005	2.838
setNodeSizeDirect	0.672	0.010	7.515
setNodeSizeRule	0.748	0.011	11.640
setNodeTooltipRule	0.741	0.012	13.444
setNodeWidthDirect	0.721	0.011	6.999
setPosition	0.686	0.009	8.958
setVisualStyle	0.858	0.014	9.162
unhideAll	0.738	0.010	7.040
unhideNodes	0.527	0.019	1.599
version	0.014	0.001	0.018