BioC 3.6: CHECK report for RCy3 on malbec1

Package: RCy3

Version: 1.7.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.7.0.tar.gz

StartedAt: 2017-08-16 01:47:42 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:48:29 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 47.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RCy3.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.7.0’
* 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-3.6-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	0	0
addCyEdge	0.004	0.000	0.000
addCyNode	0.000	0.000	0.001
addGraphToGraph	0.000	0.000	0.001
clearSelection	0.004	0.000	0.001
copyVisualStyle	0.000	0.000	0.001
createWindow	0	0	0
createWindowFromSelection	0.004	0.000	0.001
cy2.edge.names	0.000	0.000	0.001
cyPlot	0	0	0
deleteAllWindows	0.004	0.000	0.000
deleteEdgeAttribute	0.000	0.000	0.001
deleteNodeAttribute	0	0	0
deleteSelectedEdges	0.004	0.000	0.001
deleteSelectedNodes	0.000	0.000	0.001
deleteWindow	0.000	0.000	0.001
demoSimpleGraph	0	0	0
displayGraph	0	0	0
dockPanel	0	0	0
eda	0.000	0.000	0.001
eda.names	0	0	0
existing.CytoscapeWindow	0.000	0.000	0.001
fitContent	0	0	0
fitSelectedContent	0	0	0
floatPanel	0.000	0.000	0.001
getAdjacentEdgeNames	0.000	0.000	0.001
getAllEdgeAttributes	0.000	0.000	0.001
getAllEdges	0	0	0
getAllNodeAttributes	0.000	0.000	0.001
getAllNodes	0.000	0.000	0.001
getArrowShapes	0	0	0
getAttributeClassNames	0	0	0
getCenter	0.004	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	0	0
getEdgeAttribute	0.004	0.000	0.001
getEdgeAttributeNames	0.000	0.000	0.001
getEdgeCount	0	0	0
getFirstNeighbors	0.004	0.000	0.000
getGraph	0	0	0
getGraphFromCyWindow	0.000	0.000	0.001
getLayoutNameMapping	0.000	0.000	0.001
getLayoutNames	0.000	0.000	0.001
getLayoutPropertyNames	0	0	0
getLayoutPropertyType	0	0	0
getLayoutPropertyValue	0.004	0.000	0.001
getLineStyles	0	0	0
getNodeAttribute	0	0	0
getNodeAttributeNames	0.004	0.000	0.001
getNodeCount	0.000	0.000	0.001
getNodePosition	0.000	0.000	0.001
getNodeShapes	0	0	0
getNodeSize	0.000	0.000	0.001
getSelectedEdgeCount	0.000	0.000	0.001
getSelectedEdges	0	0	0
getSelectedNodeCount	0	0	0
getSelectedNodes	0.000	0.000	0.001
getViewCoordinates	0	0	0
getVisualStyleNames	0	0	0
getWindowCount	0.000	0.000	0.001
getWindowID	0.000	0.000	0.001
getWindowList	0.000	0.000	0.001
getZoom	0	0	0
hideAllPanels	0	0	0
hideNodes	0.004	0.000	0.000
hidePanel	0.000	0.000	0.001
hideSelectedEdges	0.000	0.000	0.001
hideSelectedNodes	0.004	0.000	0.000
initEdgeAttribute	0	0	0
initNodeAttribute	0.000	0.000	0.001
invertEdgeSelection	0.000	0.000	0.001
invertNodeSelection	0.000	0.000	0.001
layoutNetwork	0	0	0
lockNodeDimensions	0.000	0.000	0.001
makeRandomGraph	0.004	0.000	0.001
makeSimpleGraph	0.000	0.000	0.001
noa	0	0	0
noa.names	0	0	0
ping	0	0	0
pluginVersion	0.000	0.000	0.001
predictTimeToDisplayGraph	0.000	0.000	0.001
raiseWindow	0	0	0
redraw	0.000	0.000	0.001
restoreLayout	0.000	0.000	0.001
saveImage	0.004	0.000	0.001
saveLayout	0	0	0
saveNetwork	0.000	0.004	0.001
selectEdges	0.000	0.000	0.001
selectFirstNeighborsOfSelectedNodes	0.000	0.000	0.001
selectNodes	0.000	0.000	0.001
sendEdges	0.000	0.000	0.001
sendNodes	0.000	0.000	0.001
setCenter	0.000	0.000	0.002
setDefaultBackgroundColor	0	0	0
setDefaultEdgeColor	0	0	0
setDefaultEdgeFontSize	0.000	0.000	0.001
setDefaultEdgeLineWidth	0	0	0
setDefaultEdgeReverseSelectionColor	0	0	0
setDefaultEdgeSelectionColor	0.000	0.000	0.001
setDefaultEdgeSourceArrowColor	0.000	0.000	0.001
setDefaultEdgeTargetArrowColor	0	0	0
setDefaultNodeBorderColor	0	0	0
setDefaultNodeBorderWidth	0.000	0.000	0.001
setDefaultNodeColor	0.004	0.000	0.001
setDefaultNodeFontSize	0	0	0
setDefaultNodeLabelColor	0.000	0.000	0.001
setDefaultNodeReverseSelectionColor	0.004	0.000	0.001
setDefaultNodeSelectionColor	0.000	0.000	0.001
setDefaultNodeShape	0	0	0
setDefaultNodeSize	0	0	0
setEdgeAttributes	0.000	0.000	0.001
setEdgeAttributesDirect	0.000	0.000	0.001
setEdgeColorDirect	0	0	0
setEdgeColorRule	0.000	0.000	0.001
setEdgeFontSizeDirect	0	0	0
setEdgeLabelColorDirect	0.000	0.000	0.001
setEdgeLabelDirect	0.000	0.000	0.001
setEdgeLabelOpacityDirect	0	0	0
setEdgeLabelRule	0	0	0
setEdgeLineStyleDirect	0.000	0.000	0.001
setEdgeLineStyleRule	0	0	0
setEdgeLineWidthDirect	0.000	0.000	0.001
setEdgeLineWidthRule	0	0	0
setEdgeOpacityDirect	0	0	0
setEdgeOpacityRule	0.000	0.000	0.001
setEdgeSourceArrowColorDirect	0	0	0
setEdgeSourceArrowColorRule	0.000	0.000	0.001
setEdgeSourceArrowOpacityDirect	0	0	0
setEdgeSourceArrowRule	0.000	0.004	0.001
setEdgeSourceArrowShapeDirect	0.000	0.000	0.001
setEdgeTargetArrowColorDirect	0	0	0
setEdgeTargetArrowColorRule	0.004	0.000	0.001
setEdgeTargetArrowOpacityDirect	0	0	0
setEdgeTargetArrowRule	0.000	0.000	0.001
setEdgeTargetArrowShapeDirect	0.000	0.000	0.001
setEdgeTooltipDirect	0.000	0.000	0.001
setEdgeTooltipRule	0.004	0.000	0.001
setGraph	0.000	0.000	0.002
setLayoutProperties	0.000	0.000	0.001
setNodeAttributes	0.000	0.000	0.001
setNodeAttributesDirect	0.000	0.000	0.001
setNodeBorderColorDirect	0.000	0.004	0.001
setNodeBorderColorRule	0.000	0.000	0.001
setNodeBorderOpacityDirect	0.000	0.000	0.001
setNodeBorderWidthDirect	0.000	0.000	0.001
setNodeBorderWidthRule	0.000	0.000	0.001
setNodeColorDirect	0.000	0.000	0.001
setNodeColorRule	0.000	0.000	0.002
setNodeFillOpacityDirect	0.004	0.000	0.001
setNodeFontSizeDirect	0.000	0.000	0.001
setNodeHeightDirect	0.000	0.000	0.001
setNodeImageDirect	0.000	0.000	0.001
setNodeLabelColorDirect	0.000	0.000	0.001
setNodeLabelDirect	0.004	0.000	0.001
setNodeLabelOpacityDirect	0.000	0.000	0.001
setNodeLabelRule	0.000	0.000	0.001
setNodeOpacityDirect	0.000	0.000	0.001
setNodeOpacityRule	0.000	0.000	0.001
setNodePosition	0.004	0.000	0.001
setNodeShapeDirect	0.000	0.000	0.001
setNodeShapeRule	0.000	0.000	0.001
setNodeSizeDirect	0.000	0.000	0.001
setNodeSizeRule	0.000	0.000	0.002
setNodeTooltipRule	0.000	0.000	0.001
setNodeWidthDirect	0.000	0.000	0.001
setTooltipDismissDelay	0.000	0.000	0.001
setTooltipInitialDelay	0.004	0.000	0.001
setVisualStyle	0.000	0.000	0.001
setWindowSize	0.000	0.000	0.001
setZoom	0.000	0.000	0.001
showGraphicsDetails	0.000	0.000	0.001
unhideAll	0.000	0.000	0.001