BioC 3.5: CHECK report for RCy3 on oaxaca

Package: RCy3

Version: 1.5.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RCy3_1.5.2.tar.gz

StartedAt: 2017-03-04 07:50:56 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:51:55 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 59.0 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_1.5.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RCy3.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.2’
* 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	0.002
CytoscapeConnectionClass-class	0.001	0.000	0.001
CytoscapeWindow	0.001	0.000	0.000
CytoscapeWindowClass-class	0.001	0.000	0.001
addCyEdge	0.000	0.000	0.001
addCyNode	0	0	0
addGraphToGraph	0.001	0.001	0.001
clearSelection	0.000	0.000	0.001
copyVisualStyle	0.001	0.000	0.001
createWindow	0.001	0.000	0.001
createWindowFromSelection	0.001	0.000	0.001
cy2.edge.names	0.001	0.000	0.001
cyPlot	0.001	0.001	0.001
deleteAllWindows	0.001	0.000	0.001
deleteEdgeAttribute	0.001	0.000	0.001
deleteNodeAttribute	0.001	0.001	0.002
deleteSelectedEdges	0.001	0.000	0.001
deleteSelectedNodes	0.001	0.000	0.001
deleteWindow	0.001	0.001	0.001
demoSimpleGraph	0.001	0.000	0.001
displayGraph	0.001	0.000	0.001
dockPanel	0.001	0.001	0.001
eda	0.001	0.000	0.001
eda.names	0	0	0
existing.CytoscapeWindow	0.001	0.001	0.001
fitContent	0.001	0.000	0.001
fitSelectedContent	0.001	0.000	0.001
floatPanel	0.001	0.001	0.001
getAdjacentEdgeNames	0.001	0.000	0.001
getAllEdgeAttributes	0.002	0.000	0.002
getAllEdges	0.000	0.000	0.001
getAllNodeAttributes	0.001	0.000	0.002
getAllNodes	0.001	0.000	0.001
getArrowShapes	0.001	0.000	0.001
getAttributeClassNames	0.001	0.000	0.001
getCenter	0.001	0.000	0.001
getDefaultBackgroundColor	0.001	0.000	0.001
getDefaultEdgeReverseSelectionColor	0.000	0.001	0.001
getDefaultEdgeSelectionColor	0.000	0.000	0.001
getDefaultNodeReverseSelectionColor	0.001	0.000	0.001
getDefaultNodeSelectionColor	0	0	0
getDirectlyModifiableVisualProperties	0.001	0.001	0.001
getEdgeAttribute	0.001	0.000	0.001
getEdgeAttributeNames	0.001	0.000	0.000
getEdgeCount	0.000	0.001	0.001
getFirstNeighbors	0.001	0.000	0.001
getGraph	0.001	0.000	0.001
getGraphFromCyWindow	0.001	0.001	0.001
getLayoutNameMapping	0.001	0.000	0.001
getLayoutNames	0	0	0
getLayoutPropertyNames	0.000	0.000	0.001
getLayoutPropertyType	0.001	0.000	0.001
getLayoutPropertyValue	0.001	0.000	0.002
getLineStyles	0.001	0.000	0.001
getNodeAttribute	0.001	0.001	0.001
getNodeAttributeNames	0.000	0.000	0.001
getNodeCount	0.001	0.000	0.000
getNodePosition	0.001	0.000	0.001
getNodeShapes	0.001	0.000	0.001
getNodeSize	0.001	0.000	0.002
getSelectedEdgeCount	0.001	0.000	0.001
getSelectedEdges	0.001	0.000	0.000
getSelectedNodeCount	0.001	0.000	0.002
getSelectedNodes	0.001	0.000	0.001
getViewCoordinates	0.001	0.000	0.001
getVisualStyleNames	0.000	0.000	0.001
getWindowCount	0	0	0
getWindowID	0.001	0.000	0.001
getWindowList	0.001	0.000	0.000
getZoom	0.000	0.001	0.001
hideAllPanels	0.001	0.000	0.000
hideNodes	0.000	0.000	0.001
hidePanel	0.000	0.000	0.001
hideSelectedEdges	0.001	0.000	0.001
hideSelectedNodes	0.001	0.001	0.001
initEdgeAttribute	0.000	0.000	0.001
initNodeAttribute	0	0	0
invertEdgeSelection	0.001	0.000	0.001
invertNodeSelection	0.001	0.000	0.000
layoutNetwork	0.000	0.000	0.001
lockNodeDimensions	0.000	0.000	0.001
makeRandomGraph	0.001	0.000	0.001
makeSimpleGraph	0.001	0.000	0.002
noa	0	0	0
noa.names	0.000	0.001	0.001
ping	0	0	0
pluginVersion	0.001	0.000	0.000
predictTimeToDisplayGraph	0.001	0.000	0.001
raiseWindow	0	0	0
redraw	0.000	0.000	0.001
restoreLayout	0.001	0.000	0.001
saveImage	0.001	0.000	0.001
saveLayout	0.000	0.000	0.001
saveNetwork	0.001	0.000	0.001
selectEdges	0	0	0
selectFirstNeighborsOfSelectedNodes	0.000	0.000	0.001
selectNodes	0.001	0.000	0.000
sendEdges	0.000	0.000	0.001
sendNodes	0	0	0
setCenter	0.001	0.000	0.001
setDefaultBackgroundColor	0.001	0.000	0.001
setDefaultEdgeColor	0.001	0.000	0.001
setDefaultEdgeFontSize	0.001	0.000	0.001
setDefaultEdgeLineWidth	0.001	0.001	0.001
setDefaultEdgeReverseSelectionColor	0.000	0.000	0.001
setDefaultEdgeSelectionColor	0.001	0.000	0.001
setDefaultEdgeSourceArrowColor	0.001	0.000	0.001
setDefaultEdgeTargetArrowColor	0.001	0.001	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	0.001
setDefaultNodeLabelColor	0	0	0
setDefaultNodeReverseSelectionColor	0.001	0.000	0.001
setDefaultNodeSelectionColor	0.001	0.000	0.001
setDefaultNodeShape	0.001	0.000	0.001
setDefaultNodeSize	0.001	0.001	0.000
setEdgeAttributes	0.000	0.000	0.001
setEdgeAttributesDirect	0.001	0.000	0.001
setEdgeColorDirect	0	0	0
setEdgeColorRule	0.000	0.000	0.001
setEdgeFontSizeDirect	0.001	0.001	0.000
setEdgeLabelColorDirect	0.000	0.000	0.001
setEdgeLabelDirect	0	0	0
setEdgeLabelOpacityDirect	0.001	0.000	0.001
setEdgeLabelRule	0.000	0.000	0.001
setEdgeLineStyleDirect	0.001	0.000	0.002
setEdgeLineStyleRule	0.001	0.000	0.001
setEdgeLineWidthDirect	0.001	0.000	0.001
setEdgeLineWidthRule	0.001	0.000	0.001
setEdgeOpacityDirect	0	0	0
setEdgeOpacityRule	0.001	0.000	0.001
setEdgeSourceArrowColorDirect	0.002	0.001	0.001
setEdgeSourceArrowColorRule	0.001	0.000	0.002
setEdgeSourceArrowOpacityDirect	0.001	0.001	0.002
setEdgeSourceArrowRule	0.001	0.000	0.001
setEdgeSourceArrowShapeDirect	0.001	0.001	0.001
setEdgeTargetArrowColorDirect	0.002	0.000	0.002
setEdgeTargetArrowColorRule	0.001	0.000	0.001
setEdgeTargetArrowOpacityDirect	0.001	0.000	0.001
setEdgeTargetArrowRule	0.001	0.000	0.000
setEdgeTargetArrowShapeDirect	0.001	0.000	0.001
setEdgeTooltipDirect	0.001	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	0.002
setNodeAttributesDirect	0	0	0
setNodeBorderColorDirect	0.001	0.000	0.001
setNodeBorderColorRule	0.001	0.000	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	0.001
setNodeColorRule	0.001	0.001	0.001
setNodeFillOpacityDirect	0.001	0.000	0.001
setNodeFontSizeDirect	0.001	0.000	0.001
setNodeHeightDirect	0.001	0.000	0.002
setNodeImageDirect	0.001	0.000	0.001
setNodeLabelColorDirect	0.001	0.001	0.001
setNodeLabelDirect	0.000	0.000	0.001
setNodeLabelOpacityDirect	0	0	0
setNodeLabelRule	0.000	0.000	0.001
setNodeOpacityDirect	0.001	0.000	0.001
setNodeOpacityRule	0.001	0.000	0.001
setNodePosition	0.001	0.000	0.001
setNodeShapeDirect	0.000	0.000	0.001
setNodeShapeRule	0.001	0.000	0.001
setNodeSizeDirect	0.001	0.000	0.001
setNodeSizeRule	0.002	0.000	0.002
setNodeTooltipRule	0.001	0.000	0.001
setNodeWidthDirect	0.001	0.000	0.002
setTooltipDismissDelay	0.001	0.001	0.001
setTooltipInitialDelay	0.001	0.000	0.001
setVisualStyle	0.001	0.000	0.001
setWindowSize	0.001	0.000	0.001
setZoom	0.001	0.000	0.001
showGraphicsDetails	0.001	0.000	0.001
unhideAll	0.000	0.000	0.001