BioC 3.2: CHECK report for RCy3 on zin1

Package: RCy3

Version: 1.0.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.0.1.tar.gz

StartedAt: 2016-04-23 04:27:37 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:39:08 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 691.5 seconds

RetCode: 0

Status:  OK

CheckDir: RCy3.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RCy3.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.0.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RCy3’ can be installed ... [4s/4s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9m/11m] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
setNodeOpacityDirect            63.477  1.829  72.322
setNodeSizeDirect               44.489  1.234  50.715
getNodeSize                     42.956  1.127  49.217
setNodeLabelColorDirect         40.195  1.020  45.829
setNodeWidthDirect              23.048  0.574  26.261
setNodeShapeDirect              21.953  0.596  25.029
setNodeHeightDirect             20.733  0.588  23.690
setNodeLabelOpacityDirect       20.572  0.569  23.564
setNodeImageDirect              20.149  0.522  23.066
setNodeFillOpacityDirect        19.868  0.585  22.770
setNodeFontSizeDirect           19.736  0.527  22.592
setNodeLabelDirect              19.586  0.525  22.535
setNodeBorderOpacityDirect      18.651  0.532  21.446
setNodeColorDirect              18.642  0.459  21.988
setNodeBorderColorDirect        18.406  0.423  21.181
lockNodeDimensions              18.244  0.479  20.920
setEdgeSourceArrowShapeDirect    1.247  0.053  15.788
setEdgeTargetArrowShapeDirect    1.238  0.019  15.726
setEdgeSourceArrowColorDirect    0.699  0.019   5.276
setCenter                        0.640  0.043   5.845
setEdgeSourceArrowOpacityDirect  0.569  0.031   7.818
setWindowSize                    0.474  0.033   6.055
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [0s/0s]
 [0s/0s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/RCy3.Rcheck/00check.log’
for details.

* installing *source* package ‘RCy3’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RCy3)

name	user	system	elapsed
CytoscapeConnection	0.066	0.003	0.101
CytoscapeConnectionClass-class	0.018	0.000	0.052
CytoscapeWindow	0.053	0.008	0.217
CytoscapeWindowClass-class	0.063	0.008	0.155
addCyEdge	0.718	0.001	0.933
addCyNode	0.745	0.021	0.974
addGraphToGraph	0.825	0.020	1.077
clearSelection	0.747	0.021	0.952
copyVisualStyle	0.957	0.035	1.207
createWindowFromSelection	0.574	0.033	1.161
cy2.edge.names	0.020	0.000	0.244
cyPlot	0.393	0.020	0.585
deleteAllWindows	0.115	0.008	0.393
deleteEdgeAttribute	0.592	0.012	0.770
deleteNodeAttribute	0.626	0.012	0.822
deleteSelectedEdges	0.740	0.012	1.009
deleteSelectedNodes	0.717	0.009	0.983
deleteWindow	0.658	0.016	0.972
demoSimpleGraph	0.695	0.004	0.905
displayGraph	0.503	0.016	0.690
dockPanel	0.042	0.000	0.084
eda	0.020	0.000	0.026
eda.names	0.021	0.000	0.027
existing.CytoscapeWindow	0.459	0.028	0.627
fitContent	0.579	0.008	0.778
fitSelectedContent	0.580	0.024	0.804
floatPanel	0.046	0.000	0.148
getAdjacentEdgeNames	0.019	0.000	0.025
getAllEdgeAttributes	0.492	0.004	0.629
getAllEdges	0.470	0.009	0.665
getAllNodeAttributes	0.515	0.009	0.685
getAllNodes	0.524	0.012	0.740
getArrowShapes	0.028	0.004	0.072
getAttributeClassNames	0.016	0.000	0.026
getCenter	0.519	0.032	0.704
getDefaultBackgroundColor	0.035	0.000	0.075
getDefaultEdgeReverseSelectionColor	0.027	0.004	0.043
getDefaultEdgeSelectionColor	0.030	0.000	0.043
getDefaultNodeReverseSelectionColor	0.031	0.000	0.043
getDefaultNodeSelectionColor	0.035	0.000	0.046
getDirectlyModifiableVisualProperties	0.030	0.000	0.044
getEdgeAttribute	0.565	0.000	0.704
getEdgeAttributeNames	0.483	0.007	0.877
getEdgeCount	0.546	0.025	0.729
getFirstNeighbors	0.523	0.028	0.740
getGraph	0.450	0.012	0.617
getGraphFromCyWindow	2.085	0.053	2.534
getLayoutNameMapping	0.018	0.000	0.055
getLayoutNames	0.030	0.000	0.042
getLayoutPropertyNames	0.031	0.000	0.048
getLayoutPropertyType	0.137	0.019	0.185
getLayoutPropertyValue	0.032	0.000	0.044
getLineStyles	0.033	0.001	0.046
getNodeAttribute	0.543	0.008	0.668
getNodeAttributeNames	0.553	0.012	0.707
getNodeCount	0.495	0.024	0.682
getNodePosition	0.575	0.016	0.746
getNodeShapes	0.032	0.000	0.071
getNodeSize	42.956	1.127	49.217
getSelectedEdgeCount	0.514	0.004	0.669
getSelectedEdges	0.494	0.001	0.656
getSelectedNodeCount	0.496	0.016	0.695
getSelectedNodes	0.521	0.021	0.714
getViewCoordinates	0.452	0.016	0.609
getVisualStyleNames	0.027	0.000	0.065
getWindowCount	0.126	0.000	0.217
getWindowID	0.453	0.019	0.649
getWindowList	0.026	0.000	0.065
getZoom	0.489	0.005	0.632
hideAllPanels	0.061	0.004	0.169
hideNodes	0.570	0.007	0.700
hidePanel	0.039	0.001	0.074
hideSelectedEdges	0.138	0.004	0.194
hideSelectedNodes	0.160	0.003	0.239
initEdgeAttribute	0.013	0.000	0.039
initNodeAttribute	0.014	0.000	0.020
invertEdgeSelection	0.075	0.008	0.126
invertNodeSelection	0.198	0.004	0.289
layoutNetwork	0.551	0.009	0.696
lockNodeDimensions	18.244	0.479	20.920
makeRandomGraph	0.017	0.008	0.052
makeSimpleGraph	0.028	0.000	0.034
noa	0.021	0.000	0.026
noa.names	0.021	0.000	0.027
ping	0.030	0.000	0.041
pluginVersion	0.025	0.000	0.036
predictTimeToDisplayGraph	0.556	0.024	0.687
raiseWindow	0.053	0.000	0.129
redraw	0.062	0.000	0.132
restoreLayout	0.613	0.036	0.818
saveImage	0.486	0.036	0.657
saveLayout	0.724	0.028	0.927
saveNetwork	0.649	0.009	0.790
selectEdges	0.478	0.028	0.656
selectFirstNeighborsOfSelectedNodes	0.517	0.016	0.687
selectNodes	0.129	0.008	0.218
sendEdges	0.083	0.004	0.156
sendNodes	0.056	0.008	0.130
setCenter	0.640	0.043	5.845
setDefaultBackgroundColor	0.022	0.008	0.063
setDefaultEdgeColor	0.481	0.008	0.919
setDefaultEdgeFontSize	0.515	0.004	1.033
setDefaultEdgeLineWidth	0.472	0.008	0.814
setDefaultEdgeReverseSelectionColor	0.447	0.001	0.587
setDefaultEdgeSelectionColor	0.440	0.008	0.583
setDefaultEdgeSourceArrowColor	0.469	0.013	0.631
setDefaultEdgeTargetArrowColor	0.551	0.012	0.706
setDefaultNodeBorderColor	0.483	0.017	0.949
setDefaultNodeBorderWidth	0.462	0.024	0.950
setDefaultNodeColor	0.477	0.017	0.655
setDefaultNodeFontSize	0.480	0.012	0.940
setDefaultNodeLabelColor	0.492	0.004	0.951
setDefaultNodeReverseSelectionColor	0.433	0.032	1.017
setDefaultNodeSelectionColor	0.439	0.021	0.588
setDefaultNodeShape	0.518	0.024	0.972
setDefaultNodeSize	0.577	0.016	1.038
setEdgeAttributes	0.108	0.004	0.185
setEdgeAttributesDirect	0.118	0.004	0.200
setEdgeColorDirect	0.556	0.015	0.733
setEdgeColorRule	0.508	0.017	0.664
setEdgeFontSizeDirect	0.742	0.027	0.990
setEdgeLabelColorDirect	0.604	0.021	0.783
setEdgeLabelDirect	1.180	0.035	1.581
setEdgeLabelOpacityDirect	1.195	0.032	1.624
setEdgeLabelRule	0.478	0.028	0.645
setEdgeLineStyleDirect	1.468	0.038	2.128
setEdgeLineStyleRule	0.504	0.020	0.662
setEdgeLineWidthDirect	0.590	0.013	0.781
setEdgeLineWidthRule	0.501	0.016	0.650
setEdgeOpacityDirect	1.651	0.053	2.589
setEdgeOpacityRule	0.557	0.025	0.760
setEdgeSourceArrowColorDirect	0.699	0.019	5.276
setEdgeSourceArrowColorRule	0.077	0.008	0.167
setEdgeSourceArrowOpacityDirect	0.569	0.031	7.818
setEdgeSourceArrowRule	0.092	0.000	0.160
setEdgeSourceArrowShapeDirect	1.247	0.053	15.788
setEdgeTargetArrowColorDirect	0.680	0.020	4.935
setEdgeTargetArrowColorRule	0.087	0.000	0.153
setEdgeTargetArrowOpacityDirect	0.560	0.012	0.765
setEdgeTargetArrowRule	0.091	0.004	0.161
setEdgeTargetArrowShapeDirect	1.238	0.019	15.726
setEdgeTooltipDirect	0.504	0.011	1.668
setEdgeTooltipRule	0.446	0.041	0.652
setGraph	0.052	0.003	0.146
setLayoutProperties	0.027	0.000	0.060
setNodeAttributes	0.123	0.000	0.174
setNodeAttributesDirect	0.091	0.000	0.157
setNodeBorderColorDirect	18.406	0.423	21.181
setNodeBorderColorRule	0.120	0.008	0.203
setNodeBorderOpacityDirect	18.651	0.532	21.446
setNodeBorderWidthDirect	0.537	0.023	0.708
setNodeBorderWidthRule	0.473	0.009	0.635
setNodeColorDirect	18.642	0.459	21.988
setNodeColorRule	0.482	0.008	0.638
setNodeFillOpacityDirect	19.868	0.585	22.770
setNodeFontSizeDirect	19.736	0.527	22.592
setNodeHeightDirect	20.733	0.588	23.690
setNodeImageDirect	20.149	0.522	23.066
setNodeLabelColorDirect	40.195	1.020	45.829
setNodeLabelDirect	19.586	0.525	22.535
setNodeLabelOpacityDirect	20.572	0.569	23.564
setNodeLabelRule	0.647	0.036	0.860
setNodeOpacityDirect	63.477	1.829	72.322
setNodeOpacityRule	0.562	0.015	0.723
setNodePosition	0.538	0.020	0.731
setNodeShapeDirect	21.953	0.596	25.029
setNodeShapeRule	0.504	0.016	0.667
setNodeSizeDirect	44.489	1.234	50.715
setNodeSizeRule	0.573	0.016	0.743
setNodeTooltipRule	0.552	0.016	1.146
setNodeWidthDirect	23.048	0.574	26.261
setTooltipDismissDelay	0.586	0.028	0.770
setTooltipInitialDelay	0.498	0.031	0.678
setVisualStyle	0.781	0.016	1.163
setWindowSize	0.474	0.033	6.055
setZoom	0.615	0.052	2.829
showGraphicsDetails	0.015	0.000	0.047
unhideAll	0.621	0.009	2.751