BioC 2.9: CHECK report for RCytoscape on moscato1

Package: RCytoscape

Version: 1.3.2

Command: mkdir RCytoscape.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCytoscape.buildbin-libdir RCytoscape_1.3.2.tar.gz >RCytoscape-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=RCytoscape.buildbin-libdir --install="check:RCytoscape-install.out" --force-multiarch --no-vignettes --timings RCytoscape_1.3.2.tar.gz && mv RCytoscape.buildbin-libdir/* RCytoscape.Rcheck/ && rmdir RCytoscape.buildbin-libdir

StartedAt: 2011-07-07 06:02:33 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 06:42:33 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 2400.2 seconds

RetCode: None

Status: TIMEOUT

CheckDir: RCytoscape.Rcheck

Warnings: NA

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/RCytoscape.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'RCytoscape_unit_tests.R'
 OK
** running tests for arch 'x64'
  Running 'RCytoscape_unit_tests.R'


install for i386

* 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

add DLL for x64

* installing *source* package 'RCytoscape' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCytoscape' as RCytoscape_1.3.2.zip

* DONE (RCytoscape)

name	user	system	elapsed
CytoscapeConnection	2.56	0.08	8.74
CytoscapeConnectionClass-class	0	0	0
CytoscapeWindow	0.08	0.00	0.09
CytoscapeWindowClass-class	0.11	0.00	0.13
addCyEdge	0.31	0.02	3.76
addCyNode	0.33	0.01	3.91
addGraphToGraph	0.51	0.05	5.20
clearMsg	0.02	0.00	0.01
clearSelection	0.30	0.03	3.44
copyVisualStyle	0.39	0.00	4.41
createWindowFromSelection	2.29	0.05	6.47
cy2.edge.names	0.02	0.00	0.02
deleteAllWindows	0.36	0.00	0.57
deleteEdgeAttribute	0.39	0.00	3.75
deleteNodeAttribute	0.39	0.00	3.76
deleteSelectedEdges	0.34	0.01	3.91
deleteSelectedNodes	0.39	0.00	3.73
deleteWindow	0.55	0.00	3.96
displayGraph	0.28	0.02	3.65
dockPanel	0.00	0.00	0.03
eda	0.02	0.01	0.04
eda.names	0.01	0.00	0.01
existing.CytoscapeWindow	2.12	0.07	5.84
fitContent	0.31	0.00	3.83
fitSelectedContent	0.41	0.01	3.81
floatPanel	0.03	0.00	0.08
getAllEdgeAttributes	0.38	0.00	3.84
getAllEdges	0.04	0.00	0.12
getAllNodeAttributes	0.36	0.00	3.76
getAllNodes	0.11	0.00	0.12
getArrowShapes	0.02	0.00	0.02
getAttributeClassNames	0	0	0
getCenter	0.34	0.00	3.84
getDefaultBackgroundColor	0.01	0.00	0.01
getDefaultEdgeReverseSelectionColor	0.02	0.00	0.02
getDefaultEdgeSelectionColor	0.00	0.00	0.01
getDefaultNodeReverseSelectionColor	0.02	0.00	0.02
getDefaultNodeSelectionColor	0.00	0.00	0.02
getDirectlyModifiableVisualProperties	0.03	0.00	0.03
getEdgeAttribute	0.28	0.00	3.71
getEdgeAttributeNames	0.00	0.00	0.02
getEdgeCount	0.33	0.02	3.72
getFirstNeighbors	0.37	0.00	3.70
getGraph	0.12	0.00	0.14
getGraphFromCyWindow	2.24	0.04	6.23
getLayoutNameMapping	0.03	0.00	0.03
getLayoutNames	0.01	0.00	0.01
getLayoutPropertyNames	0.02	0.00	0.02
getLayoutPropertyType	0.08	0.00	0.14
getLayoutPropertyValue	0.09	0.00	0.11
getLineStyles	0.01	0.00	0.02
getNodeAttribute	0.36	0.00	3.70
getNodeAttributeNames	0.02	0.00	0.03
getNodeCount	0.42	0.00	3.79
getNodeShapes	0.01	0.00	0.01
getPosition	0.35	0.00	3.69
getSelectedEdgeCount	0.40	0.02	3.97
getSelectedEdges	0.33	0.03	3.75
getSelectedNodeCount	0.44	0.00	3.85
getSelectedNodes	0.40	0.00	3.96
getViewCoordinates	0.50	0.00	4.09
getVisualStyleNames	0	0	0
getWindowCount	0.34	0.03	0.43
getWindowID	0.47	0.00	3.57
getWindowList	0.11	0.00	0.11
getZoom	0.34	0.02	3.78
hideAllPanels	0.28	0.03	0.62
hideNodes	0.19	0.01	0.24
hidePanel	0.00	0.00	0.03
hideSelectedEdges	0.24	0.00	0.55
hideSelectedNodes	0.19	0.00	0.56
initEdgeAttribute	0	0	0
initNodeAttribute	0	0	0
invertEdgeSelection	0.19	0.00	0.22
invertNodeSelection	0.18	0.02	0.23
layout	0.39	0.00	3.88
lockNodeDimensions	0.41	0.00	3.84
makeRandomGraph	0.03	0.00	0.03
makeSimpleGraph	0.04	0.00	0.05
msg	0.02	0.00	0.01
new.CytoscapeWindow	0.25	0.00	0.28
noa	0.01	0.00	0.02
noa.names	0.04	0.00	0.03
ping	0	0	0
raiseWindow	0.17	0.00	0.22
redraw	0.18	0.00	0.20
saveImage	0.39	0.02	3.79
saveNetwork	0.35	0.01	3.79
selectEdges	0.43	0.00	4.14
selectFirstNeighborsOfSelectedNodes	0.55	0.00	3.99
selectNodes	0.25	0.02	0.30
sendEdges	0.22	0.00	1.26
sendNodes	0.22	0.00	0.26
setCenter	0.45	0.00	9.75
setDefaultBackgroundColor	0.01	0.00	0.02
setDefaultEdgeColor	0.44	0.00	3.81
setDefaultEdgeLineWidth	0.45	0.01	4.02
setDefaultEdgeReverseSelectionColor	0.02	0.00	0.03
setDefaultEdgeSelectionColor	0.01	0.00	0.02
setDefaultNodeBorderColor	0.58	0.00	3.97
setDefaultNodeBorderWidth	0.64	0.02	4.05
setDefaultNodeColor	0.67	0.00	4.04
setDefaultNodeFontSize	0.62	0.03	4.17
setDefaultNodeLabelColor	0.58	0.00	3.93
setDefaultNodeReverseSelectionColor	0.01	0.00	0.01
setDefaultNodeSelectionColor	0.02	0.00	0.02
setDefaultNodeShape	0.45	0.02	3.82
setDefaultNodeSize	0.44	0.00	3.81
setEdgeAttributes	0.30	0.00	2.35
setEdgeAttributesDirect	0.29	0.01	1.36
setEdgeColorDirect	0.53	0.00	4.00
setEdgeColorRule	0.38	0.00	4.02
setEdgeFontSizeDirect	1.45	0.02	5.21
setEdgeLabelColorDirect	0.58	0.00	3.99
setEdgeLabelDirect	1.34	0.04	4.98
setEdgeLabelOpacityDirect	1.54	0.02	5.09
setEdgeLabelRule	0.47	0.01	3.90
setEdgeLabelWidthDirect	1.56	0.05	5.21
setEdgeLineStyleDirect	1.53	0.02	5.30
setEdgeLineStyleRule	0.36	0.00	1.40
setEdgeLineWidthDirect	1.01	0.01	4.53
setEdgeLineWidthRule	0.64	0.00	5.04
setEdgeOpacityDirect	1.12	0.05	4.80
setEdgeSourceArrowColorDirect	0.62	0.00	10.37
setEdgeSourceArrowColorRule	0.32	0.00	1.34
setEdgeSourceArrowOpacityDirect	0.81	0.01	11.55
setEdgeSourceArrowRule	0.39	0.00	1.44
setEdgeSourceArrowShapeDirect	0.94	0.05	13.76
setEdgeTargetArrowColorDirect	0.75	0.03	10.34
setEdgeTargetArrowColorRule	0.45	0.00	1.50
setEdgeTargetArrowOpacityDirect	1.00	0.00	4.62
setEdgeTargetArrowRule	0.33	0.00	1.35
setEdgeTargetArrowShapeDirect	0.82	0.02	13.62
setEdgeTooltipDirect	0.59	0.01	5.10
setEdgeTooltipRule	0.5	0.0	4.9
setGraph	0.49	0.00	0.50
setLayoutProperties	0.09	0.00	0.09
setNodeAttributes	0.48	0.00	0.55
setNodeBorderColorRule	0.36	0.00	2.45
setNodeBorderOpacityDirect	0.77	0.02	4.26
setNodeBorderWidthRule	0.58	0.00	5.01
setNodeColorDirect	0.64	0.00	4.01
setNodeColorRule	0.41	0.00	2.45
setNodeFillOpacityDirect	0.71	0.02	4.13
setNodeFontSizeDirect	0.80	0.01	4.45
setNodeHeightDirect	0.67	0.00	4.04
setNodeImageDirect	0.90	0.00	4.29
setNodeLabelDirect	0.79	0.00	4.17
setNodeLabelOpacityDirect	0.49	0.00	4.19
setNodeLabelRule	0.64	0.02	4.14
setNodeOpacityDirect	0.61	0.01	3.99
setNodeShapeDirect	0.59	0.02	3.99
setNodeShapeRule	0.39	0.01	1.48
setNodeSizeDirect	0.56	0.02	4.07
setNodeSizeRule	0.91	0.00	7.37
setNodeTooltipRule	0.82	0.01	7.28
setNodeWidthDirect	0.67	0.02	4.12
setNotAttributesDirect	0.63	0.00	0.64
setPosition	0.89	0.00	5.40
setVisualStyle	1.11	0.05	7.56
setWindowSize	0.85	0.04	6.65
setZoom	0.74	0.03	6.49
showGraphicsDetails	0.00	0.00	0.01
unhideAll	0.78	0.00	4.61
unhideNodes	0.53	0.00	1.73
validCyWin	0.56	0.00	0.59
version	0.02	0.00	0.01

Summary

Command output