BioC 3.2: CHECK report for RCy3 on linux1.bioconductor.org

Package: RCy3

Version: 1.0.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.0.0.tar.gz

StartedAt: 2015-10-14 08:04:42 -0400 (Wed, 14 Oct 2015)

EndedAt: 2015-10-14 08:44:42 -0400 (Wed, 14 Oct 2015)

EllapsedTime: 2400.0 seconds

RetCode: None

Status:  TIMEOUT

CheckDir: RCy3.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RCy3.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RCy3’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...

* installing *source* package ‘RCy3’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (RCy3)

name	user	system	elapsed
CytoscapeConnection	0.076	0.003	0.137
CytoscapeConnectionClass-class	0.027	0.000	0.038
CytoscapeWindow	0.060	0.005	0.110
CytoscapeWindowClass-class	0.124	0.000	0.209
addCyEdge	0.990	0.012	1.171
addCyNode	0.825	0.017	1.003
addGraphToGraph	0.752	0.004	0.952
clearSelection	0.638	0.012	0.804
copyVisualStyle	1.010	0.012	1.225
createWindowFromSelection	0.963	0.016	1.440
cy2.edge.names	0.033	0.000	0.106
cyPlot	0.644	0.020	0.767
deleteAllWindows	0.196	0.004	0.417
deleteEdgeAttribute	0.957	0.008	1.128
deleteNodeAttribute	0.905	0.016	1.091
deleteSelectedEdges	0.962	0.008	1.387
deleteSelectedNodes	0.635	0.012	2.331
deleteWindow	0.625	0.016	0.890
demoSimpleGraph	0.773	0.021	0.963
displayGraph	0.562	0.016	0.736
dockPanel	0.075	0.000	0.114
eda	0.021	0.000	0.027
eda.names	0.022	0.000	0.028
existing.CytoscapeWindow	0.535	0.024	0.693
fitContent	0.828	0.017	1.041
fitSelectedContent	1.007	0.004	1.203
floatPanel	0.076	0.000	0.165
getAdjacentEdgeNames	0.032	0.000	0.038
getAllEdgeAttributes	0.848	0.008	0.986
getAllEdges	0.800	0.032	0.993
getAllNodeAttributes	0.852	0.004	1.003
getAllNodes	0.815	0.017	0.974
getArrowShapes	0.047	0.000	0.089
getAttributeClassNames	0.027	0.000	0.038
getCenter	0.898	0.012	1.047
getDefaultBackgroundColor	0.042	0.004	0.084
getDefaultEdgeReverseSelectionColor	0.038	0.000	0.050
getDefaultEdgeSelectionColor	0.048	0.000	0.060
getDefaultNodeReverseSelectionColor	0.046	0.000	0.058
getDefaultNodeSelectionColor	0.042	0.000	0.056
getDirectlyModifiableVisualProperties	0.047	0.000	0.062
getEdgeAttribute	0.755	0.003	0.890
getEdgeAttributeNames	0.555	0.008	1.075
getEdgeCount	0.567	0.017	0.728
getFirstNeighbors	0.687	0.016	0.866
getGraph	0.660	0.025	1.061
getGraphFromCyWindow	2.409	0.028	2.817
getLayoutNameMapping	0.017	0.000	0.057
getLayoutNames	0.029	0.000	0.042
getLayoutPropertyNames	0.028	0.000	0.041
getLayoutPropertyType	0.130	0.016	0.177
getLayoutPropertyValue	0.032	0.000	0.045
getLineStyles	0.029	0.000	0.040
getNodeAttribute	0.785	0.012	1.588
getNodeAttributeNames	0.530	0.004	0.675
getNodeCount	0.761	0.025	1.172
getNodePosition	0.877	0.012	1.022
getNodeShapes	0.045	0.000	0.085
getNodeSize	1307.360	19.615	1467.820
getSelectedEdgeCount	0.642	0.016	1.487
getSelectedEdges	0.527	0.004	0.698
getSelectedNodeCount	0.791	0.025	1.541
getSelectedNodes	0.828	0.020	1.028
getViewCoordinates	0.527	0.004	1.238
getVisualStyleNames	0.028	0.000	0.066
getWindowCount	0.138	0.001	0.243
getWindowID	0.509	0.016	0.694
getWindowList	0.030	0.000	0.067
getZoom	0.791	0.012	1.450
hideAllPanels	0.111	0.004	0.343
hideNodes	0.990	0.036	1.447
hidePanel	0.072	0.000	0.106
hideSelectedEdges	0.225	0.012	0.288
hideSelectedNodes	0.276	0.004	0.352
initEdgeAttribute	0.023	0.000	0.053
initNodeAttribute	0.024	0.000	0.029
invertEdgeSelection	0.133	0.000	0.179
invertNodeSelection	0.280	0.008	0.375
layoutNetwork	0.808	0.000	1.183
lockNodeDimensions	445.876	6.835	497.912
makeRandomGraph	0.034	0.000	0.062
makeSimpleGraph	0.039	0.000	0.045
noa	0.030	0.000	0.035
noa.names	0.028	0.000	0.035
ping	0.045	0.000	0.057
pluginVersion	0.039	0.000	0.051
predictTimeToDisplayGraph	0.766	0.024	1.112
raiseWindow	0.086	0.000	0.148
redraw	0.109	0.000	0.164
restoreLayout	1.131	0.012	1.541
saveImage	0.771	0.020	0.919
saveLayout	1.236	0.004	1.658
saveNetwork	0.797	0.012	1.158
selectEdges	0.956	0.008	1.102
selectFirstNeighborsOfSelectedNodes	0.871	0.028	1.273
selectNodes	0.222	0.008	0.295
sendEdges	0.130	0.000	0.418
sendNodes	0.097	0.000	0.162
setCenter	0.991	0.021	6.410
setDefaultBackgroundColor	0.036	0.008	0.078
setDefaultEdgeColor	0.841	0.020	1.544
setDefaultEdgeFontSize	0.865	0.013	1.254
setDefaultEdgeLineWidth	0.846	0.015	1.234
setDefaultEdgeReverseSelectionColor	0.795	0.000	1.152
setDefaultEdgeSelectionColor	0.789	0.004	1.152
setDefaultEdgeSourceArrowColor	0.841	0.001	1.454
setDefaultEdgeTargetArrowColor	0.809	0.008	1.184
setDefaultNodeBorderColor	0.776	0.016	1.186
setDefaultNodeBorderWidth	0.843	0.003	1.453
setDefaultNodeColor	0.849	0.009	1.491
setDefaultNodeFontSize	0.594	0.008	0.978
setDefaultNodeLabelColor	0.673	0.017	1.289
setDefaultNodeReverseSelectionColor	0.794	0.012	1.386
setDefaultNodeSelectionColor	0.786	0.020	1.160
setDefaultNodeShape	0.874	0.028	1.720
setDefaultNodeSize	0.823	0.020	1.440
setEdgeAttributes	0.145	0.000	0.444
setEdgeAttributesDirect	0.151	0.000	0.223
setEdgeColorDirect	0.839	0.019	1.750
setEdgeColorRule	0.895	0.016	1.969
setEdgeFontSizeDirect	0.915	0.000	3.425
setEdgeLabelColorDirect	0.652	0.012	1.952
setEdgeLabelDirect	1.639	0.036	5.373
setEdgeLabelOpacityDirect	1.806	0.029	6.029
setEdgeLabelRule	0.768	0.005	2.258
setEdgeLineStyleDirect	2.064	0.012	8.584
setEdgeLineStyleRule	0.861	0.008	3.700
setEdgeLineWidthDirect	0.811	0.008	7.746
setEdgeLineWidthRule	0.766	0.008	10.572
setEdgeOpacityDirect	2.845	0.045	200.863