BioC 3.5: CHECK report for RCy3 on veracruz2

Package: RCy3

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RCy3_1.6.0.tar.gz

StartedAt: 2017-10-18 07:59:24 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 08:00:23 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 59.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RCy3.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RCy3_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RCy3.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.0’
* 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 ... 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 ... 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 ... WARNING
Undocumented code objects:
  ‘copyCytoscapeNetwork’ ‘renameCytoscapeNetwork’ ‘selectAllEdges’
  ‘selectAllNodes’
Undocumented S4 methods:
  generic 'copyCytoscapeNetwork' and siglist 'CytoscapeWindowClass'
  generic 'renameCytoscapeNetwork' and siglist 'CytoscapeWindowClass'
  generic 'selectAllEdges' and siglist 'CytoscapeWindowClass'
  generic 'selectAllNodes' and siglist 'CytoscapeWindowClass'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-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	0.001	0.000	0.001
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.001	0.000	0.001
CytoscapeWindowClass-class	0.001	0.001	0.001
addCyEdge	0.001	0.000	0.001
addCyNode	0.001	0.000	0.001
addGraphToGraph	0.001	0.001	0.002
clearSelection	0.001	0.000	0.000
copyVisualStyle	0.002	0.000	0.002
createWindow	0.001	0.001	0.001
createWindowFromSelection	0.001	0.000	0.000
cy2.edge.names	0.001	0.000	0.001
cyPlot	0.001	0.000	0.001
deleteAllWindows	0.000	0.000	0.001
deleteEdgeAttribute	0.001	0.000	0.001
deleteNodeAttribute	0.000	0.000	0.001
deleteSelectedEdges	0.001	0.000	0.001
deleteSelectedNodes	0.001	0.000	0.000
deleteWindow	0.001	0.000	0.002
demoSimpleGraph	0.001	0.000	0.001
displayGraph	0.001	0.000	0.001
dockPanel	0.001	0.000	0.001
eda	0.001	0.000	0.001
eda.names	0.001	0.000	0.001
existing.CytoscapeWindow	0.001	0.000	0.001
fitContent	0.001	0.001	0.001
fitSelectedContent	0	0	0
floatPanel	0.001	0.000	0.001
getAdjacentEdgeNames	0.001	0.001	0.001
getAllEdgeAttributes	0.001	0.000	0.002
getAllEdges	0.000	0.000	0.001
getAllNodeAttributes	0.001	0.001	0.001
getAllNodes	0.001	0.000	0.001
getArrowShapes	0.001	0.000	0.001
getAttributeClassNames	0.001	0.001	0.001
getCenter	0.000	0.000	0.001
getDefaultBackgroundColor	0.001	0.000	0.001
getDefaultEdgeReverseSelectionColor	0.001	0.000	0.001
getDefaultEdgeSelectionColor	0.001	0.000	0.001
getDefaultNodeReverseSelectionColor	0.001	0.001	0.001
getDefaultNodeSelectionColor	0.001	0.000	0.001
getDirectlyModifiableVisualProperties	0.001	0.000	0.001
getEdgeAttribute	0.001	0.001	0.001
getEdgeAttributeNames	0.001	0.000	0.001
getEdgeCount	0.001	0.000	0.001
getFirstNeighbors	0.001	0.001	0.001
getGraph	0.001	0.000	0.001
getGraphFromCyWindow	0.001	0.000	0.001
getLayoutNameMapping	0.001	0.000	0.001
getLayoutNames	0.001	0.000	0.000
getLayoutPropertyNames	0.001	0.000	0.001
getLayoutPropertyType	0.001	0.000	0.002
getLayoutPropertyValue	0.002	0.000	0.001
getLineStyles	0.001	0.001	0.001
getNodeAttribute	0.001	0.000	0.001
getNodeAttributeNames	0.001	0.000	0.001
getNodeCount	0.000	0.001	0.001
getNodePosition	0.000	0.000	0.001
getNodeShapes	0.001	0.000	0.001
getNodeSize	0.001	0.001	0.001
getSelectedEdgeCount	0.002	0.000	0.001
getSelectedEdges	0.001	0.001	0.001
getSelectedNodeCount	0.001	0.000	0.001
getSelectedNodes	0.001	0.000	0.001
getViewCoordinates	0.001	0.000	0.001
getVisualStyleNames	0.000	0.000	0.001
getWindowCount	0.000	0.000	0.002
getWindowID	0.001	0.000	0.000
getWindowList	0.001	0.000	0.001
getZoom	0.001	0.000	0.001
hideAllPanels	0.001	0.000	0.001
hideNodes	0.001	0.000	0.001
hidePanel	0.001	0.000	0.001
hideSelectedEdges	0.001	0.000	0.001
hideSelectedNodes	0.001	0.000	0.001
initEdgeAttribute	0.001	0.000	0.001
initNodeAttribute	0.001	0.000	0.001
invertEdgeSelection	0.001	0.000	0.001
invertNodeSelection	0.001	0.000	0.001
layoutNetwork	0.001	0.000	0.002
lockNodeDimensions	0.001	0.000	0.001
makeRandomGraph	0.001	0.001	0.001
makeSimpleGraph	0.002	0.001	0.003
noa	0.001	0.000	0.001
noa.names	0.000	0.000	0.001
ping	0.000	0.000	0.001
pluginVersion	0.000	0.000	0.001
predictTimeToDisplayGraph	0.001	0.000	0.001
raiseWindow	0.001	0.000	0.001
redraw	0.001	0.001	0.001
restoreLayout	0.001	0.000	0.001
saveImage	0.001	0.000	0.001
saveLayout	0.001	0.000	0.001
saveNetwork	0.001	0.000	0.001
selectEdges	0.001	0.000	0.002
selectFirstNeighborsOfSelectedNodes	0.001	0.000	0.001
selectNodes	0.001	0.000	0.001
sendEdges	0.001	0.000	0.001
sendNodes	0.001	0.001	0.001
setCenter	0.001	0.000	0.001
setDefaultBackgroundColor	0.000	0.000	0.001
setDefaultEdgeColor	0.000	0.000	0.001
setDefaultEdgeFontSize	0.001	0.001	0.001
setDefaultEdgeLineWidth	0.001	0.000	0.001
setDefaultEdgeReverseSelectionColor	0.001	0.000	0.001
setDefaultEdgeSelectionColor	0.001	0.000	0.001
setDefaultEdgeSourceArrowColor	0.000	0.000	0.001
setDefaultEdgeTargetArrowColor	0.001	0.000	0.001
setDefaultNodeBorderColor	0.001	0.000	0.001
setDefaultNodeBorderWidth	0.001	0.000	0.001
setDefaultNodeColor	0.001	0.000	0.001
setDefaultNodeFontSize	0.001	0.000	0.002
setDefaultNodeLabelColor	0.000	0.000	0.001
setDefaultNodeReverseSelectionColor	0.001	0.001	0.002
setDefaultNodeSelectionColor	0.001	0.000	0.000
setDefaultNodeShape	0.001	0.001	0.001
setDefaultNodeSize	0.001	0.000	0.001
setEdgeAttributes	0.000	0.000	0.001
setEdgeAttributesDirect	0.001	0.000	0.001
setEdgeColorDirect	0.001	0.000	0.001
setEdgeColorRule	0.001	0.000	0.001
setEdgeFontSizeDirect	0.000	0.000	0.001
setEdgeLabelColorDirect	0.001	0.001	0.001
setEdgeLabelDirect	0.001	0.000	0.001
setEdgeLabelOpacityDirect	0.001	0.001	0.002
setEdgeLabelRule	0.001	0.000	0.001
setEdgeLineStyleDirect	0.002	0.001	0.001
setEdgeLineStyleRule	0.001	0.000	0.001
setEdgeLineWidthDirect	0.001	0.000	0.002
setEdgeLineWidthRule	0.000	0.000	0.001
setEdgeOpacityDirect	0.001	0.000	0.000
setEdgeOpacityRule	0.001	0.000	0.002
setEdgeSourceArrowColorDirect	0.001	0.000	0.002
setEdgeSourceArrowColorRule	0.002	0.000	0.001
setEdgeSourceArrowOpacityDirect	0.001	0.000	0.001
setEdgeSourceArrowRule	0.001	0.000	0.001
setEdgeSourceArrowShapeDirect	0.002	0.000	0.002
setEdgeTargetArrowColorDirect	0.001	0.000	0.002
setEdgeTargetArrowColorRule	0.001	0.000	0.001
setEdgeTargetArrowOpacityDirect	0.002	0.000	0.002
setEdgeTargetArrowRule	0.001	0.001	0.001
setEdgeTargetArrowShapeDirect	0.001	0.000	0.001
setEdgeTooltipDirect	0.001	0.001	0.001
setEdgeTooltipRule	0.001	0.000	0.001
setGraph	0.001	0.000	0.001
setLayoutProperties	0.001	0.000	0.001
setNodeAttributes	0.001	0.000	0.001
setNodeAttributesDirect	0.001	0.001	0.001
setNodeBorderColorDirect	0.001	0.000	0.002
setNodeBorderColorRule	0.002	0.000	0.002
setNodeBorderOpacityDirect	0.001	0.000	0.001
setNodeBorderWidthDirect	0.001	0.000	0.001
setNodeBorderWidthRule	0.001	0.000	0.001
setNodeColorDirect	0.001	0.000	0.001
setNodeColorRule	0.002	0.001	0.001
setNodeFillOpacityDirect	0.001	0.000	0.001
setNodeFontSizeDirect	0.001	0.001	0.001
setNodeHeightDirect	0.001	0.000	0.001
setNodeImageDirect	0.001	0.000	0.001
setNodeLabelColorDirect	0.001	0.000	0.001
setNodeLabelDirect	0.001	0.000	0.001
setNodeLabelOpacityDirect	0.001	0.000	0.002
setNodeLabelRule	0.001	0.000	0.001
setNodeOpacityDirect	0.001	0.000	0.001
setNodeOpacityRule	0.001	0.000	0.002
setNodePosition	0.001	0.001	0.001
setNodeShapeDirect	0	0	0
setNodeShapeRule	0.001	0.000	0.001
setNodeSizeDirect	0.001	0.000	0.001
setNodeSizeRule	0.001	0.000	0.002
setNodeTooltipRule	0.001	0.000	0.001
setNodeWidthDirect	0.001	0.000	0.001
setTooltipDismissDelay	0.000	0.000	0.001
setTooltipInitialDelay	0.001	0.000	0.001
setVisualStyle	0.001	0.000	0.001
setWindowSize	0.001	0.001	0.000
setZoom	0.001	0.000	0.001
showGraphicsDetails	0.001	0.000	0.001
unhideAll	0.000	0.000	0.001