BioC 3.3: CHECK report for RCy3 on zin2

Package: RCy3

Version: 1.2.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.2.0.tar.gz

StartedAt: 2016-10-13 05:49:28 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:52:07 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 158.9 seconds

RetCode: 0

Status:  OK

CheckDir: RCy3.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RCy3.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.2.0’
* 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 ... 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 ... 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 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 ... NOTE
.BBSOverride: no visible global function definition for ‘as’
is.classic.graph: no visible global function definition for ‘is’
is.multiGraph: no visible global function definition for ‘is’
Undefined global functions or variables:
  as is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
hideSelectedEdges 7.789  0.072   9.125
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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	0.057	0.008	0.100
CytoscapeConnectionClass-class	0.015	0.001	0.028
CytoscapeWindow	0.055	0.001	0.126
CytoscapeWindowClass-class	0.063	0.005	0.157
addCyEdge	0.461	0.003	0.705
addCyNode	0.495	0.005	0.715
addGraphToGraph	0.765	0.004	1.026
clearSelection	0.842	0.004	1.093
copyVisualStyle	0.685	0.008	0.938
createWindow	0.067	0.000	0.936
createWindowFromSelection	1.421	0.020	2.425
cy2.edge.names	0.017	0.000	0.079
cyPlot	0.313	0.000	0.513
deleteAllWindows	0.095	0.000	0.803
deleteEdgeAttribute	0.427	0.016	0.612
deleteNodeAttribute	0.455	0.016	0.655
deleteSelectedEdges	0.510	0.008	0.736
deleteSelectedNodes	0.492	0.016	0.731
deleteWindow	0.498	0.008	0.860
demoSimpleGraph	0.537	0.008	0.705
displayGraph	0.435	0.007	0.630
dockPanel	0.045	0.000	0.108
eda	0.017	0.000	0.023
eda.names	0.016	0.000	0.023
existing.CytoscapeWindow	1.566	0.036	1.978
fitContent	0.501	0.000	0.716
fitSelectedContent	0.434	0.004	0.633
floatPanel	0.047	0.000	0.175
getAdjacentEdgeNames	0.017	0.000	0.023
getAllEdgeAttributes	0.376	0.004	0.526
getAllEdges	0.370	0.008	0.560
getAllNodeAttributes	0.456	0.004	0.645
getAllNodes	0.360	0.013	0.558
getArrowShapes	0.023	0.000	0.067
getAttributeClassNames	0.015	0.004	0.028
getCenter	0.387	0.012	0.560
getDefaultBackgroundColor	0.025	0.000	0.067
getDefaultEdgeReverseSelectionColor	0.022	0.000	0.034
getDefaultEdgeSelectionColor	0.021	0.000	0.033
getDefaultNodeReverseSelectionColor	0.022	0.000	0.035
getDefaultNodeSelectionColor	0.024	0.000	0.036
getDirectlyModifiableVisualProperties	0.027	0.000	0.041
getEdgeAttribute	0.524	0.000	0.684
getEdgeAttributeNames	0.606	0.012	0.787
getEdgeCount	0.527	0.016	0.707
getFirstNeighbors	0.412	0.005	0.604
getGraph	0.333	0.012	0.532
getGraphFromCyWindow	1.584	0.012	2.099
getLayoutNameMapping	0.126	0.004	0.295
getLayoutNames	0.025	0.000	0.052
getLayoutPropertyNames	0.027	0.000	0.040
getLayoutPropertyType	0.122	0.004	0.151
getLayoutPropertyValue	0.102	0.000	0.127
getLineStyles	0.019	0.004	0.034
getNodeAttribute	0.400	0.004	0.532
getNodeAttributeNames	0.379	0.012	0.550
getNodeCount	0.470	0.000	0.662
getNodePosition	0.512	0.000	0.669
getNodeShapes	0.031	0.000	0.071
getNodeSize	0.878	0.024	1.078
getSelectedEdgeCount	0.432	0.008	0.628
getSelectedEdges	0.481	0.020	0.675
getSelectedNodeCount	0.450	0.009	0.657
getSelectedNodes	0.472	0.000	0.627
getViewCoordinates	0.387	0.008	0.600
getVisualStyleNames	0.022	0.000	0.065
getWindowCount	0.119	0.005	0.238
getWindowID	0.446	0.015	0.643
getWindowList	0.141	0.005	0.284
getZoom	0.373	0.007	0.801
hideAllPanels	0.057	0.000	0.209
hideNodes	0.626	0.008	0.816
hidePanel	0.045	0.000	0.081
hideSelectedEdges	7.789	0.072	9.125
hideSelectedNodes	0.647	0.009	0.852
initEdgeAttribute	0.012	0.000	0.040
initNodeAttribute	0.012	0.000	0.018
invertEdgeSelection	0.372	0.011	0.505
invertNodeSelection	0.561	0.028	0.780
layoutNetwork	0.378	0.012	0.702
lockNodeDimensions	0.439	0.008	0.597
makeRandomGraph	0.020	0.000	0.048
makeSimpleGraph	0.022	0.000	0.029
noa	0.016	0.000	0.021
noa.names	0.016	0.000	0.022
ping	0.022	0.000	0.033
pluginVersion	0.015	0.004	0.031
predictTimeToDisplayGraph	0.345	0.004	0.458
raiseWindow	0.083	0.000	0.199
redraw	0.491	0.008	0.702
restoreLayout	0.635	0.004	0.941
saveImage	0.373	0.000	0.595
saveLayout	0.558	0.008	0.778
saveNetwork	0.367	0.016	0.545
selectEdges	0.420	0.008	0.598
selectFirstNeighborsOfSelectedNodes	0.494	0.008	0.667
selectNodes	0.426	0.000	0.592
sendEdges	0.071	0.000	0.160
sendNodes	0.056	0.000	0.124
setCenter	0.484	0.038	1.182
setDefaultBackgroundColor	0.104	0.000	0.232
setDefaultEdgeColor	0.368	0.008	0.558
setDefaultEdgeFontSize	0.419	0.001	0.904
setDefaultEdgeLineWidth	0.349	0.004	0.832
setDefaultEdgeReverseSelectionColor	0.356	0.004	0.522
setDefaultEdgeSelectionColor	0.352	0.004	0.500
setDefaultEdgeSourceArrowColor	0.384	0.000	0.760
setDefaultEdgeTargetArrowColor	0.373	0.012	0.522
setDefaultNodeBorderColor	0.365	0.004	0.511
setDefaultNodeBorderWidth	0.361	0.004	0.843
setDefaultNodeColor	0.361	0.000	0.830
setDefaultNodeFontSize	0.364	0.000	0.813
setDefaultNodeLabelColor	0.36	0.00	1.08
setDefaultNodeReverseSelectionColor	0.370	0.004	0.852
setDefaultNodeSelectionColor	0.357	0.004	0.820
setDefaultNodeShape	0.379	0.004	0.519
setDefaultNodeSize	0.371	0.004	0.821
setEdgeAttributes	0.227	0.016	0.644
setEdgeAttributesDirect	0.095	0.004	0.173
setEdgeColorDirect	0.354	0.012	0.567
setEdgeColorRule	0.402	0.004	0.547
setEdgeFontSizeDirect	0.890	0.012	1.192
setEdgeLabelColorDirect	0.524	0.001	0.700
setEdgeLabelDirect	0.617	0.000	0.877
setEdgeLabelOpacityDirect	0.745	0.012	1.003
setEdgeLabelRule	0.356	0.008	0.504
setEdgeLineStyleDirect	0.958	0.004	1.298
setEdgeLineStyleRule	0.378	0.008	0.526
setEdgeLineWidthDirect	0.541	0.024	0.781
setEdgeLineWidthRule	0.364	0.000	0.499
setEdgeOpacityDirect	0.725	0.012	0.983
setEdgeOpacityRule	0.433	0.000	0.610
setEdgeSourceArrowColorDirect	0.482	0.004	1.896
setEdgeSourceArrowColorRule	0.418	0.012	0.632
setEdgeSourceArrowOpacityDirect	0.382	0.000	0.533
setEdgeSourceArrowRule	0.364	0.009	0.533
setEdgeSourceArrowShapeDirect	0.478	0.003	0.685
setEdgeTargetArrowColorDirect	0.526	0.000	1.906
setEdgeTargetArrowColorRule	0.401	0.004	0.567
setEdgeTargetArrowOpacityDirect	0.370	0.013	0.896
setEdgeTargetArrowRule	0.366	0.004	0.548
setEdgeTargetArrowShapeDirect	0.452	0.012	0.626
setEdgeTooltipDirect	0.418	0.000	0.587
setEdgeTooltipRule	0.351	0.008	0.499
setGraph	0.355	0.000	0.707
setLayoutProperties	0.051	0.004	0.110
setNodeAttributes	0.196	0.004	0.269
setNodeAttributesDirect	0.076	0.000	0.147
setNodeBorderColorDirect	0.446	0.004	0.595
setNodeBorderColorRule	0.449	0.000	0.621
setNodeBorderOpacityDirect	0.379	0.004	0.847
setNodeBorderWidthDirect	0.367	0.004	0.502
setNodeBorderWidthRule	0.366	0.000	0.500
setNodeColorDirect	0.379	0.008	0.845
setNodeColorRule	0.381	0.008	0.518
setNodeFillOpacityDirect	0.410	0.004	1.185
setNodeFontSizeDirect	0.416	0.004	0.577
setNodeHeightDirect	0.456	0.008	0.613
setNodeImageDirect	0.351	0.012	0.502
setNodeLabelColorDirect	0.515	0.004	0.663
setNodeLabelDirect	0.419	0.004	0.579
setNodeLabelOpacityDirect	0.466	0.012	0.615
setNodeLabelRule	0.432	0.004	0.583
setNodeOpacityDirect	0.566	0.016	0.765
setNodeOpacityRule	0.422	0.008	0.565
setNodePosition	0.408	0.009	0.584
setNodeShapeDirect	0.450	0.012	0.607
setNodeShapeRule	0.407	0.011	0.554
setNodeSizeDirect	0.533	0.012	0.753
setNodeSizeRule	0.550	0.012	0.705
setNodeTooltipRule	0.544	0.020	0.777
setNodeWidthDirect	0.499	0.004	0.761
setTooltipDismissDelay	0.411	0.008	0.576
setTooltipInitialDelay	0.419	0.004	0.589
setVisualStyle	0.393	0.008	0.524
setWindowSize	0.364	0.008	0.489
setZoom	0.392	0.038	1.196
showGraphicsDetails	0.020	0.004	0.054
unhideAll	0.518	0.010	1.165