Package: RCytoscape

Version: 1.1.53

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RCytoscape_1.1.53.tar.gz

StartedAt: 2011-03-17 17:15:27 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:38:52 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 1405.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RCytoscape.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/RCytoscape.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '1.1.53'
* 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 ... 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 contents of 'data' directory ... WARNING
Files not of a type allowed in a 'data' directory:
  galFiltered.cys
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 were 2 warnings, 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	0.076	0.005	0.268
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.052	0.002	0.154
CytoscapeWindowClass-class	0.093	0.003	0.222
addCyEdge	0.339	0.009	6.879
addCyNode	0.297	0.007	6.593
addGraphToGraph	0.430	0.011	9.021
clearMsg	0.009	0.001	0.012
clearSelection	0.301	0.007	6.394
copyVisualStyle	0.344	0.009	7.769
createWindowFromSelection	1.218	0.032	8.333
cy2.edge.names	0.019	0.000	0.020
deleteAllWindows	0.291	0.007	1.012
deleteEdgeAttribute	0.294	0.007	6.629
deleteNodeAttribute	0.302	0.007	6.391
deleteSelectedEdges	0.323	0.008	6.628
deleteSelectedNodes	0.320	0.008	6.651
deleteWindow	0.380	0.008	6.770
displayGraph	0.276	0.006	6.586
dockPanel	0.022	0.000	0.044
eda	0.063	0.000	0.062
eda.names	0.018	0.000	0.019
existing.CytoscapeWindow	0.935	0.024	7.136
fitContent	0.310	0.008	6.612
fitSelectedContent	0.342	0.009	6.677
floatPanel	0.020	0.001	0.065
getAllEdgeAttributes	0.294	0.006	6.588
getAllEdges	0.084	0.001	0.117
getAllNodeAttributes	0.287	0.007	6.567
getAllNodes	0.098	0.002	0.132
getArrowShapes	0.011	0.001	0.014
getAttributeClassNames	0.001	0.000	0.001
getCenter	0.298	0.007	6.584
getDefaultBackgroundColor	0.010	0.001	0.013
getDefaultEdgeReverseSelectionColor	0.011	0.000	0.013
getDefaultEdgeSelectionColor	0.010	0.000	0.013
getDefaultNodeReverseSelectionColor	0.011	0.001	0.013
getDefaultNodeSelectionColor	0.010	0.001	0.014
getDirectlyModifiableVisualProperties	0.025	0.001	0.028
getEdgeAttribute	0.326	0.008	6.646
getEdgeAttributeNames	0.011	0.000	0.014
getEdgeCount	0.303	0.006	6.583
getFirstNeighbors	0.353	0.008	6.707
getGraph	0.107	0.002	0.139
getGraphFromCyWindow	1.034	0.024	7.489
getLayoutNameMapping	0.033	0.000	0.035
getLayoutNames	0.014	0.000	0.017
getLayoutPropertyNames	0.012	0.000	0.016
getLayoutPropertyType	0.095	0.003	0.120
getLayoutPropertyValue	0.102	0.003	0.122
getLineStyles	0.015	0.000	0.017
getNodeAttribute	0.333	0.008	6.670
getNodeAttributeNames	0.011	0.001	0.014
getNodeCount	0.331	0.007	6.630
getNodeShapes	0.013	0.000	0.017
getPosition	0.319	0.006	6.615
getSelectedEdgeCount	0.354	0.007	6.661
getSelectedEdges	0.340	0.007	6.662
getSelectedNodeCount	0.373	0.009	6.718
getSelectedNodes	0.390	0.008	6.681
getViewCoordinates	0.351	0.007	6.644
getVisualStyleNames	0.013	0.001	0.016
getWindowCount	0.327	0.005	0.452
getWindowID	0.395	0.006	6.457
getWindowList	0.101	0.002	0.108
getZoom	0.343	0.007	6.676
hideAllPanels	0.238	0.008	0.410
hideNodes	0.199	0.003	0.242
hidePanel	0.020	0.000	0.024
hideSelectedEdges	0.200	0.003	0.489
hideSelectedNodes	0.234	0.005	0.530
initEdgeAttribute	0.003	0.000	0.002
initNodeAttribute	0.003	0.000	0.003
invertEdgeSelection	0.178	0.003	0.228
invertNodeSelection	0.208	0.004	0.260
layout	0.349	0.006	6.642
lockNodeDimensions	0.412	0.009	6.773
makeRandomGraph	0.018	0.000	0.017
makeSimpleGraph	0.024	0.000	0.024
msg	0.011	0.000	0.016
new.CytoscapeWindow	0.153	0.002	0.189
noa	0.018	0.000	0.019
noa.names	0.02	0.00	0.02
ping	0.010	0.001	0.012
raiseWindow	0.182	0.002	0.213
redraw	0.215	0.002	0.277
saveImage	0.557	0.009	7.031
selectEdges	0.566	0.010	6.972
selectFirstNeighborsOfSelectedNodes	0.523	0.011	6.864
selectNodes	0.246	0.003	0.291
sendEdgeAttributes	0.242	0.003	4.278
sendEdgeAttributesDirect	0.214	0.002	2.247
sendEdges	0.224	0.002	2.259
sendNodeAttributes	0.266	0.003	0.308
sendNodeAttributesDirect	0.220	0.002	0.252
sendNodes	0.209	0.001	0.240
setCenter	0.485	0.018	11.870
setDefaultBackgroundColor	0.011	0.001	0.013
setDefaultEdgeColor	0.425	0.007	6.720
setDefaultEdgeLineWidth	0.434	0.007	6.730
setDefaultEdgeReverseSelectionColor	0.011	0.000	0.013
setDefaultEdgeSelectionColor	0.011	0.001	0.013
setDefaultNodeBorderColor	0.441	0.007	6.736
setDefaultNodeBorderWidth	0.434	0.006	7.796
setDefaultNodeColor	0.427	0.006	6.731
setDefaultNodeFontSize	0.446	0.007	6.740
setDefaultNodeLabelColor	0.495	0.008	6.806
setDefaultNodeReverseSelectionColor	0.011	0.001	0.013
setDefaultNodeSelectionColor	0.012	0.001	0.014
setDefaultNodeShape	0.461	0.009	6.813
setDefaultNodeSize	0.455	0.008	6.767
setEdgeColorRule	0.331	0.004	7.283
setEdgeLabelRule	0.434	0.007	6.852
setEdgeLineStyleRule	0.255	0.002	2.293
setEdgeLineWidthRule	0.451	0.009	8.758
setEdgeSourceArrowColorRule	0.265	0.002	2.299
setEdgeSourceArrowRule	0.261	0.002	2.296
setEdgeTargetArrowColorRule	0.260	0.002	2.291
setEdgeTargetArrowRule	0.289	0.003	2.350
setEdgeTooltipRule	0.479	0.008	8.786
setGraph	0.259	0.002	0.285
setLayoutProperties	0.054	0.002	0.067
setNodeBorderColorRule	0.323	0.003	4.365
setNodeBorderOpacityDirect	0.485	0.007	6.790
setNodeBorderWidthRule	0.489	0.007	8.989
setNodeColorDirect	0.496	0.007	6.803
setNodeColorRule	0.337	0.005	4.389
setNodeFillOpacityDirect	0.499	0.007	6.813
setNodeHeightDirect	0.519	0.007	6.851
setNodeLabelOpacityDirect	0.505	0.007	6.909
setNodeLabelRule	0.634	0.012	6.993
setNodeOpacityDirect	0.526	0.008	6.845
setNodeShapeDirect	0.532	0.008	6.858
setNodeShapeRule	0.325	0.003	2.372
setNodeSizeDirect	0.529	0.007	6.935
setNodeSizeRule	0.567	0.009	10.892
setNodeTooltipRule	0.546	0.009	12.872
setNodeWidthDirect	0.550	0.008	6.862
setPosition	0.551	0.007	8.945
setVisualStyle	0.653	0.012	9.885
setWindowSize	0.582	0.013	8.924
setZoom	0.548	0.014	8.880
unhideAll	0.564	0.010	7.011
unhideNodes	0.381	0.005	1.436
version	0.008	0.000	0.011