BioC 3.5: CHECK report for RCy3 on malbec2

Package: RCy3

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.6.0.tar.gz

StartedAt: 2017-08-16 01:41:14 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:42:02 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 47.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RCy3.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/RCy3.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.6.0’
* 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 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
  ‘/home/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	0.000	0.000	0.001
CytoscapeConnectionClass-class	0	0	0
CytoscapeWindow	0	0	0
CytoscapeWindowClass-class	0.000	0.000	0.001
addCyEdge	0.000	0.000	0.001
addCyNode	0.000	0.000	0.001
addGraphToGraph	0.004	0.000	0.001
clearSelection	0.000	0.000	0.001
copyVisualStyle	0	0	0
createWindow	0.000	0.000	0.001
createWindowFromSelection	0.000	0.000	0.001
cy2.edge.names	0	0	0
cyPlot	0.000	0.000	0.001
deleteAllWindows	0	0	0
deleteEdgeAttribute	0	0	0
deleteNodeAttribute	0.000	0.000	0.001
deleteSelectedEdges	0.000	0.000	0.001
deleteSelectedNodes	0	0	0
deleteWindow	0.004	0.000	0.001
demoSimpleGraph	0.000	0.000	0.001
displayGraph	0.000	0.000	0.001
dockPanel	0.000	0.000	0.001
eda	0	0	0
eda.names	0.000	0.000	0.001
existing.CytoscapeWindow	0.000	0.000	0.001
fitContent	0.000	0.000	0.001
fitSelectedContent	0	0	0
floatPanel	0	0	0
getAdjacentEdgeNames	0.000	0.000	0.001
getAllEdgeAttributes	0.000	0.000	0.001
getAllEdges	0	0	0
getAllNodeAttributes	0.004	0.000	0.001
getAllNodes	0	0	0
getArrowShapes	0	0	0
getAttributeClassNames	0.004	0.000	0.000
getCenter	0.000	0.000	0.001
getDefaultBackgroundColor	0.000	0.000	0.001
getDefaultEdgeReverseSelectionColor	0.000	0.000	0.001
getDefaultEdgeSelectionColor	0	0	0
getDefaultNodeReverseSelectionColor	0	0	0
getDefaultNodeSelectionColor	0	0	0
getDirectlyModifiableVisualProperties	0.000	0.000	0.001
getEdgeAttribute	0	0	0
getEdgeAttributeNames	0	0	0
getEdgeCount	0.004	0.000	0.001
getFirstNeighbors	0.000	0.000	0.001
getGraph	0.000	0.000	0.001
getGraphFromCyWindow	0.004	0.000	0.000
getLayoutNameMapping	0	0	0
getLayoutNames	0	0	0
getLayoutPropertyNames	0.000	0.000	0.001
getLayoutPropertyType	0	0	0
getLayoutPropertyValue	0.000	0.000	0.001
getLineStyles	0.000	0.000	0.001
getNodeAttribute	0.000	0.000	0.001
getNodeAttributeNames	0	0	0
getNodeCount	0	0	0
getNodePosition	0.000	0.000	0.001
getNodeShapes	0.000	0.000	0.001
getNodeSize	0.000	0.000	0.001
getSelectedEdgeCount	0.004	0.000	0.001
getSelectedEdges	0.000	0.000	0.001
getSelectedNodeCount	0	0	0
getSelectedNodes	0.004	0.000	0.000
getViewCoordinates	0.000	0.000	0.001
getVisualStyleNames	0.000	0.000	0.001
getWindowCount	0	0	0
getWindowID	0	0	0
getWindowList	0	0	0
getZoom	0.000	0.000	0.001
hideAllPanels	0	0	0
hideNodes	0	0	0
hidePanel	0	0	0
hideSelectedEdges	0.000	0.000	0.001
hideSelectedNodes	0.000	0.000	0.001
initEdgeAttribute	0	0	0
initNodeAttribute	0.004	0.000	0.000
invertEdgeSelection	0.000	0.000	0.001
invertNodeSelection	0.000	0.000	0.001
layoutNetwork	0	0	0
lockNodeDimensions	0	0	0
makeRandomGraph	0.000	0.000	0.001
makeSimpleGraph	0.004	0.000	0.001
noa	0	0	0
noa.names	0	0	0
ping	0.004	0.000	0.000
pluginVersion	0	0	0
predictTimeToDisplayGraph	0.000	0.000	0.001
raiseWindow	0.000	0.000	0.001
redraw	0	0	0
restoreLayout	0	0	0
saveImage	0.000	0.000	0.001
saveLayout	0.000	0.000	0.001
saveNetwork	0.000	0.000	0.001
selectEdges	0	0	0
selectFirstNeighborsOfSelectedNodes	0.004	0.000	0.001
selectNodes	0.000	0.000	0.001
sendEdges	0.000	0.000	0.001
sendNodes	0	0	0
setCenter	0.000	0.000	0.001
setDefaultBackgroundColor	0.000	0.000	0.001
setDefaultEdgeColor	0.004	0.000	0.000
setDefaultEdgeFontSize	0	0	0
setDefaultEdgeLineWidth	0.000	0.000	0.001
setDefaultEdgeReverseSelectionColor	0.000	0.000	0.001
setDefaultEdgeSelectionColor	0	0	0
setDefaultEdgeSourceArrowColor	0	0	0
setDefaultEdgeTargetArrowColor	0.000	0.000	0.001
setDefaultNodeBorderColor	0.000	0.000	0.001
setDefaultNodeBorderWidth	0	0	0
setDefaultNodeColor	0	0	0
setDefaultNodeFontSize	0.000	0.000	0.001
setDefaultNodeLabelColor	0.000	0.000	0.001
setDefaultNodeReverseSelectionColor	0	0	0
setDefaultNodeSelectionColor	0.004	0.000	0.000
setDefaultNodeShape	0.000	0.000	0.001
setDefaultNodeSize	0.004	0.000	0.001
setEdgeAttributes	0.000	0.000	0.001
setEdgeAttributesDirect	0	0	0
setEdgeColorDirect	0.004	0.000	0.000
setEdgeColorRule	0.000	0.000	0.001
setEdgeFontSizeDirect	0	0	0
setEdgeLabelColorDirect	0.004	0.000	0.000
setEdgeLabelDirect	0.000	0.000	0.001
setEdgeLabelOpacityDirect	0.000	0.000	0.001
setEdgeLabelRule	0.004	0.000	0.000
setEdgeLineStyleDirect	0.000	0.000	0.001
setEdgeLineStyleRule	0	0	0
setEdgeLineWidthDirect	0.004	0.000	0.001
setEdgeLineWidthRule	0.000	0.000	0.001
setEdgeOpacityDirect	0.000	0.000	0.001
setEdgeOpacityRule	0.004	0.000	0.000
setEdgeSourceArrowColorDirect	0.000	0.000	0.001
setEdgeSourceArrowColorRule	0	0	0
setEdgeSourceArrowOpacityDirect	0.000	0.000	0.001
setEdgeSourceArrowRule	0	0	0
setEdgeSourceArrowShapeDirect	0.000	0.000	0.001
setEdgeTargetArrowColorDirect	0	0	0
setEdgeTargetArrowColorRule	0.000	0.000	0.001
setEdgeTargetArrowOpacityDirect	0.004	0.000	0.000
setEdgeTargetArrowRule	0.000	0.000	0.001
setEdgeTargetArrowShapeDirect	0.000	0.000	0.001
setEdgeTooltipDirect	0.004	0.000	0.001
setEdgeTooltipRule	0.000	0.000	0.001
setGraph	0.000	0.000	0.001
setLayoutProperties	0.004	0.000	0.000
setNodeAttributes	0.000	0.000	0.001
setNodeAttributesDirect	0.000	0.000	0.001
setNodeBorderColorDirect	0.000	0.000	0.001
setNodeBorderColorRule	0	0	0
setNodeBorderOpacityDirect	0.000	0.000	0.001
setNodeBorderWidthDirect	0.000	0.000	0.001
setNodeBorderWidthRule	0.000	0.000	0.001
setNodeColorDirect	0	0	0
setNodeColorRule	0.000	0.000	0.001
setNodeFillOpacityDirect	0.000	0.000	0.001
setNodeFontSizeDirect	0	0	0
setNodeHeightDirect	0.000	0.000	0.001
setNodeImageDirect	0.000	0.000	0.001
setNodeLabelColorDirect	0	0	0
setNodeLabelDirect	0	0	0
setNodeLabelOpacityDirect	0.000	0.000	0.001
setNodeLabelRule	0	0	0
setNodeOpacityDirect	0	0	0
setNodeOpacityRule	0.000	0.000	0.001
setNodePosition	0	0	0
setNodeShapeDirect	0	0	0
setNodeShapeRule	0.004	0.000	0.001
setNodeSizeDirect	0.000	0.000	0.001
setNodeSizeRule	0.000	0.000	0.001
setNodeTooltipRule	0.000	0.000	0.001
setNodeWidthDirect	0	0	0
setTooltipDismissDelay	0.000	0.000	0.001
setTooltipInitialDelay	0.000	0.000	0.001
setVisualStyle	0	0	0
setWindowSize	0.000	0.000	0.001
setZoom	0.000	0.000	0.001
showGraphicsDetails	0	0	0
unhideAll	0	0	0