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: 2017-08-16 07:12:36 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:13:32 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 55.3 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 3.4.1 (2017-06-30)
* 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	0	0
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.000	0.001	0.001
CytoscapeWindowClass-class	0.001	0.000	0.000
addCyEdge	0.001	0.000	0.001
addCyNode	0.000	0.000	0.001
addGraphToGraph	0.002	0.001	0.002
clearSelection	0	0	0
copyVisualStyle	0.001	0.000	0.001
createWindow	0.000	0.000	0.001
createWindowFromSelection	0.001	0.000	0.001
cy2.edge.names	0.001	0.000	0.000
cyPlot	0	0	0
deleteAllWindows	0.001	0.000	0.001
deleteEdgeAttribute	0.001	0.000	0.001
deleteNodeAttribute	0.001	0.000	0.000
deleteSelectedEdges	0.001	0.000	0.001
deleteSelectedNodes	0	0	0
deleteWindow	0.000	0.000	0.001
demoSimpleGraph	0.000	0.000	0.001
displayGraph	0	0	0
dockPanel	0.001	0.000	0.001
eda	0.000	0.000	0.001
eda.names	0.001	0.000	0.000
existing.CytoscapeWindow	0.001	0.000	0.001
fitContent	0.001	0.000	0.001
fitSelectedContent	0.001	0.001	0.001
floatPanel	0.000	0.000	0.001
getAdjacentEdgeNames	0.000	0.000	0.001
getAllEdgeAttributes	0.001	0.000	0.001
getAllEdges	0	0	0
getAllNodeAttributes	0.000	0.000	0.001
getAllNodes	0.001	0.000	0.001
getArrowShapes	0.001	0.000	0.000
getAttributeClassNames	0.000	0.001	0.001
getCenter	0.001	0.000	0.001
getDefaultBackgroundColor	0.000	0.000	0.001
getDefaultEdgeReverseSelectionColor	0.001	0.000	0.000
getDefaultEdgeSelectionColor	0.001	0.000	0.001
getDefaultNodeReverseSelectionColor	0.001	0.000	0.001
getDefaultNodeSelectionColor	0.000	0.000	0.001
getDirectlyModifiableVisualProperties	0.000	0.000	0.001
getEdgeAttribute	0.001	0.001	0.001
getEdgeAttributeNames	0	0	0
getEdgeCount	0.000	0.000	0.001
getFirstNeighbors	0.000	0.000	0.001
getGraph	0.001	0.000	0.000
getGraphFromCyWindow	0.001	0.000	0.001
getLayoutNameMapping	0.000	0.000	0.001
getLayoutNames	0.001	0.000	0.001
getLayoutPropertyNames	0.000	0.000	0.001
getLayoutPropertyType	0.001	0.000	0.001
getLayoutPropertyValue	0.001	0.001	0.001
getLineStyles	0	0	0
getNodeAttribute	0.001	0.000	0.004
getNodeAttributeNames	0.000	0.000	0.001
getNodeCount	0.001	0.000	0.001
getNodePosition	0.000	0.000	0.001
getNodeShapes	0.001	0.000	0.001
getNodeSize	0.002	0.000	0.002
getSelectedEdgeCount	0	0	0
getSelectedEdges	0.001	0.000	0.001
getSelectedNodeCount	0.001	0.000	0.000
getSelectedNodes	0.000	0.000	0.001
getViewCoordinates	0	0	0
getVisualStyleNames	0.001	0.000	0.001
getWindowCount	0.000	0.000	0.001
getWindowID	0.001	0.000	0.001
getWindowList	0.001	0.000	0.000
getZoom	0.001	0.000	0.001
hideAllPanels	0	0	0
hideNodes	0.000	0.000	0.001
hidePanel	0.001	0.000	0.001
hideSelectedEdges	0.001	0.001	0.001
hideSelectedNodes	0.001	0.000	0.001
initEdgeAttribute	0.000	0.000	0.001
initNodeAttribute	0.001	0.000	0.000
invertEdgeSelection	0.001	0.000	0.001
invertNodeSelection	0.000	0.001	0.001
layoutNetwork	0	0	0
lockNodeDimensions	0.001	0.000	0.001
makeRandomGraph	0.001	0.000	0.002
makeSimpleGraph	0.001	0.000	0.001
noa	0.000	0.000	0.001
noa.names	0.000	0.000	0.001
ping	0	0	0
pluginVersion	0.001	0.000	0.001
predictTimeToDisplayGraph	0.001	0.000	0.001
raiseWindow	0.001	0.000	0.001
redraw	0.001	0.000	0.000
restoreLayout	0.000	0.000	0.001
saveImage	0.000	0.001	0.000
saveLayout	0.000	0.000	0.001
saveNetwork	0.001	0.000	0.000
selectEdges	0.001	0.000	0.001
selectFirstNeighborsOfSelectedNodes	0	0	0
selectNodes	0.001	0.000	0.001
sendEdges	0.000	0.000	0.001
sendNodes	0.001	0.000	0.000
setCenter	0.001	0.000	0.001
setDefaultBackgroundColor	0.000	0.001	0.000
setDefaultEdgeColor	0.000	0.000	0.001
setDefaultEdgeFontSize	0.001	0.000	0.000
setDefaultEdgeLineWidth	0.001	0.000	0.001
setDefaultEdgeReverseSelectionColor	0.001	0.000	0.001
setDefaultEdgeSelectionColor	0	0	0
setDefaultEdgeSourceArrowColor	0.000	0.000	0.001
setDefaultEdgeTargetArrowColor	0.000	0.000	0.001
setDefaultNodeBorderColor	0.001	0.000	0.000
setDefaultNodeBorderWidth	0.001	0.000	0.001
setDefaultNodeColor	0.001	0.000	0.001
setDefaultNodeFontSize	0	0	0
setDefaultNodeLabelColor	0.000	0.000	0.001
setDefaultNodeReverseSelectionColor	0.001	0.000	0.000
setDefaultNodeSelectionColor	0.001	0.000	0.001
setDefaultNodeShape	0.001	0.000	0.001
setDefaultNodeSize	0.001	0.000	0.001
setEdgeAttributes	0	0	0
setEdgeAttributesDirect	0.001	0.000	0.001
setEdgeColorDirect	0	0	0
setEdgeColorRule	0.002	0.001	0.002
setEdgeFontSizeDirect	0.001	0.000	0.002
setEdgeLabelColorDirect	0	0	0
setEdgeLabelDirect	0.001	0.001	0.000
setEdgeLabelOpacityDirect	0.001	0.000	0.001
setEdgeLabelRule	0.001	0.000	0.001
setEdgeLineStyleDirect	0.000	0.001	0.001
setEdgeLineStyleRule	0.001	0.000	0.000
setEdgeLineWidthDirect	0.001	0.000	0.001
setEdgeLineWidthRule	0.000	0.000	0.001
setEdgeOpacityDirect	0.001	0.000	0.001
setEdgeOpacityRule	0.002	0.000	0.002
setEdgeSourceArrowColorDirect	0.001	0.000	0.002
setEdgeSourceArrowColorRule	0.002	0.001	0.002
setEdgeSourceArrowOpacityDirect	0.001	0.000	0.001
setEdgeSourceArrowRule	0.000	0.000	0.001
setEdgeSourceArrowShapeDirect	0.001	0.001	0.002
setEdgeTargetArrowColorDirect	0.001	0.000	0.001
setEdgeTargetArrowColorRule	0.001	0.000	0.002
setEdgeTargetArrowOpacityDirect	0.001	0.000	0.001
setEdgeTargetArrowRule	0.000	0.000	0.001
setEdgeTargetArrowShapeDirect	0.002	0.001	0.002
setEdgeTooltipDirect	0.000	0.000	0.001
setEdgeTooltipRule	0.001	0.000	0.001
setGraph	0.000	0.000	0.001
setLayoutProperties	0.001	0.000	0.001
setNodeAttributes	0.001	0.000	0.001
setNodeAttributesDirect	0.001	0.000	0.001
setNodeBorderColorDirect	0.001	0.000	0.001
setNodeBorderColorRule	0.001	0.001	0.001
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	0.000
setNodeColorRule	0.000	0.000	0.001
setNodeFillOpacityDirect	0.001	0.000	0.001
setNodeFontSizeDirect	0.001	0.000	0.001
setNodeHeightDirect	0.001	0.000	0.002
setNodeImageDirect	0	0	0
setNodeLabelColorDirect	0.001	0.000	0.001
setNodeLabelDirect	0	0	0
setNodeLabelOpacityDirect	0.001	0.000	0.001
setNodeLabelRule	0.001	0.000	0.001
setNodeOpacityDirect	0.001	0.000	0.000
setNodeOpacityRule	0.001	0.000	0.001
setNodePosition	0	0	0
setNodeShapeDirect	0.001	0.000	0.001
setNodeShapeRule	0.001	0.000	0.000
setNodeSizeDirect	0.001	0.000	0.001
setNodeSizeRule	0.001	0.000	0.002
setNodeTooltipRule	0	0	0
setNodeWidthDirect	0.001	0.001	0.002
setTooltipDismissDelay	0.001	0.000	0.000
setTooltipInitialDelay	0.000	0.000	0.001
setVisualStyle	0.001	0.000	0.003
setWindowSize	0.001	0.000	0.001
setZoom	0.001	0.000	0.001
showGraphicsDetails	0.000	0.000	0.001
unhideAll	0.001	0.001	0.001