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 16:38:38 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 16:59:21 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 1243.0 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: ASCII
* 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	0.104	0.003	0.159
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.050	0.002	0.089
CytoscapeWindowClass-class	0.090	0.002	0.128
addCyEdge	0.366	0.012	6.667
addCyNode	0.297	0.009	6.577
addGraphToGraph	0.407	0.011	8.947
clearMsg	0.009	0.001	0.013
clearSelection	0.292	0.009	6.379
copyVisualStyle	0.338	0.010	7.116
cy.sfn	0.368	0.010	6.681
cy2.edge.names	0.019	0.000	0.019
deleteEdgeAttribute	0.318	0.008	6.617
deleteNodeAttribute	0.309	0.009	6.585
destroyAllWindows	0.146	0.005	0.347
destroyWindow	0.088	0.003	0.134
displayGraph	0.242	0.007	6.513
dockPanel	0.018	0.001	0.025
eda	0.019	0.001	0.020
eda.names	0.017	0.000	0.017
existing.CytoscapeWindow	0.948	0.025	7.576
firstNeighbors	0.062	0.001	0.092
floatPanel	0.019	0.001	0.074
getAllEdgeAttributes	0.275	0.007	6.545
getAllEdges	0.072	0.002	0.104
getAllNodeAttributes	0.280	0.006	6.592
getAllNodes	0.080	0.001	0.114
getArrowShapes	0.011	0.001	0.014
getAttributeClassNames	0.001	0.000	0.001
getDefaultBackgroundColor	0.010	0.000	0.013
getDefaultEdgeReverseSelectionColor	0.010	0.001	0.012
getDefaultEdgeSelectionColor	0.009	0.000	0.012
getDefaultNodeReverseSelectionColor	0.011	0.000	0.013
getDefaultNodeSelectionColor	0.009	0.001	0.012
getDirectlyModifiableVisualProperties	0.018	0.001	0.021
getEdgeAttribute	0.287	0.007	6.647
getEdgeAttributeNames	0.011	0.000	0.014
getEdgeCount	0.281	0.006	6.554
getGraph	0.085	0.002	0.116
getGraphFromCyWindow	0.955	0.023	7.401
getLayoutNames	0.016	0.001	0.018
getLineStyles	0.013	0.000	0.016
getNodeAttribute	0.307	0.008	6.616
getNodeAttributeNames	0.014	0.001	0.017
getNodeCount	0.312	0.008	6.581
getNodeShapes	0.016	0.001	0.018
getPosition	0.316	0.008	6.586
getSelectedEdgeCount	0.349	0.009	6.617
getSelectedEdges	0.321	0.008	6.624
getSelectedNodeCount	0.342	0.008	6.622
getSelectedNodes	0.394	0.011	6.682
getVisualStyleNames	0.012	0.000	0.014
getWindowCount	0.247	0.004	0.320
getWindowID	0.362	0.007	6.426
getWindowList	0.079	0.001	0.085
hideAllPanels	0.238	0.008	0.416
hideNodes	0.166	0.003	0.228
hidePanel	0.019	0.001	0.024
hideSelectedEdges	0.177	0.004	0.744
hideSelectedNodes	0.212	0.004	0.488
initEdgeAttribute	0.002	0.000	0.002
initNodeAttribute	0.002	0.000	0.002
invertEdgeSelection	0.156	0.003	0.203
invertNodeSelection	0.178	0.003	0.239
layout	0.326	0.007	6.603
lockNodeDimensions	0.373	0.009	6.654
makeRandomGraph	0.017	0.000	0.017
makeSimpleGraph	0.024	0.001	0.025
msg	0.010	0.001	0.013
new.CytoscapeWindow	0.126	0.002	0.161
noa	0.02	0.00	0.02
noa.names	0.017	0.001	0.017
ping	0.010	0.000	0.012
raiseWindow	0.154	0.002	0.191
redraw	0.157	0.003	0.191
removeSelectedEdges	0.194	0.003	0.234
removeSelectedNodes	0.191	0.004	0.231
resizeWindow	0.353	0.007	6.672
saveImage	0.363	0.007	6.634
selectEdge	0.431	0.009	6.750
selectEdges	0.422	0.010	6.769
selectNodes	0.225	0.003	0.268
sendEdgeAttributes	0.239	0.003	4.276
sendEdgeAttributesDirect	0.186	0.002	2.548
sendEdges	0.210	0.003	2.261
sendNodeAttributes	0.241	0.003	0.283
sendNodeAttributesDirect	0.195	0.002	0.224
sendNodes	0.196	0.003	0.342
setDefaultBackgroundColor	0.012	0.000	0.015
setDefaultEdgeColor	0.418	0.008	6.779
setDefaultEdgeLineWidth	0.408	0.007	6.678
setDefaultEdgeReverseSelectionColor	0.011	0.001	0.014
setDefaultEdgeSelectionColor	0.011	0.001	0.014
setDefaultNodeBorderColor	0.417	0.008	6.701
setDefaultNodeBorderWidth	0.424	0.008	6.763
setDefaultNodeColor	0.431	0.007	6.729
setDefaultNodeFontSize	0.433	0.008	6.708
setDefaultNodeLabelColor	0.441	0.009	6.716
setDefaultNodeReverseSelectionColor	0.014	0.001	0.018
setDefaultNodeSelectionColor	0.011	0.001	0.014
setDefaultNodeShape	0.454	0.008	6.799
setDefaultNodeSize	0.473	0.010	6.795
setEdgeColorRule	0.321	0.005	6.508
setEdgeLabelRule	0.432	0.007	6.723
setEdgeLineStyleRule	0.252	0.003	2.287
setEdgeLineWidthRule	0.437	0.007	8.714
setEdgeSourceArrowColorRule	0.248	0.002	2.280
setEdgeSourceArrowRule	0.258	0.003	2.292
setEdgeTargetArrowColorRule	0.253	0.002	2.287
setEdgeTargetArrowRule	0.263	0.003	2.299
setEdgeTooltipRule	0.551	0.010	8.989
setGraph	0.378	0.003	0.452
setNodeBorderColorRule	0.431	0.005	4.557
setNodeBorderOpacityDirect	0.457	0.007	6.749
setNodeBorderWidthRule	0.473	0.009	8.757
setNodeColorDirect	0.473	0.008	6.764
setNodeColorRule	0.327	0.004	4.371
setNodeFillOpacityDirect	0.483	0.008	7.180
setNodeHeightDirect	0.508	0.008	6.793
setNodeLabelOpacityDirect	0.485	0.007	6.775
setNodeLabelRule	0.602	0.011	7.011
setNodeOpacityDirect	0.526	0.010	6.830
setNodeShapeDirect	0.508	0.008	6.833
setNodeShapeRule	0.327	0.005	2.508
setNodeSizeDirect	0.490	0.008	6.791
setNodeSizeRule	0.555	0.009	10.936
setNodeTooltipRule	0.534	0.008	12.835
setNodeWidthDirect	0.539	0.009	6.832
setPosition	0.519	0.007	8.797
setVisualStyle	0.637	0.012	8.696
unhideAll	0.561	0.009	7.011
unhideNodes	0.401	0.007	1.464
version	0.009	0.001	0.011