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BioC 3.4: CHECK report for RCy3 on tokay1

This page was generated on 2017-04-15 16:20:28 -0400 (Sat, 15 Apr 2017).

Package 1015/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 1.5.2
Tanja Muetze , Georgi Kolishovski , Paul Shannon
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/RCy3
Last Changed Rev: 125580 / Revision: 128728
Last Changed Date: 2017-01-03 03:24:02 -0500 (Tue, 03 Jan 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCy3
Version: 1.5.2
Command: rm -rf RCy3.buildbin-libdir RCy3.Rcheck && mkdir RCy3.buildbin-libdir RCy3.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCy3.buildbin-libdir RCy3_1.5.2.tar.gz >RCy3.Rcheck\00install.out 2>&1 && cp RCy3.Rcheck\00install.out RCy3-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RCy3.buildbin-libdir --install="check:RCy3-install.out" --force-multiarch --no-vignettes --timings RCy3_1.5.2.tar.gz
StartedAt: 2017-04-15 00:23:23 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:24:38 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 75.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RCy3.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RCy3.buildbin-libdir RCy3.Rcheck && mkdir RCy3.buildbin-libdir RCy3.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RCy3.buildbin-libdir RCy3_1.5.2.tar.gz >RCy3.Rcheck\00install.out 2>&1 && cp RCy3.Rcheck\00install.out RCy3-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RCy3.buildbin-libdir --install="check:RCy3-install.out" --force-multiarch --no-vignettes --timings RCy3_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/RCy3.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/RCy3.Rcheck/00check.log'
for details.


RCy3.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'RCy3' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCy3' as RCy3_1.5.2.zip
* DONE (RCy3)

RCy3.Rcheck/examples_i386/RCy3-Ex.timings:

nameusersystemelapsed
CytoscapeConnection000
CytoscapeConnectionClass-class000
CytoscapeWindow000
CytoscapeWindowClass-class000
addCyEdge000
addCyNode000
addGraphToGraph000
clearSelection000
copyVisualStyle000
createWindow000
createWindowFromSelection000
cy2.edge.names000
cyPlot000
deleteAllWindows000
deleteEdgeAttribute000
deleteNodeAttribute000
deleteSelectedEdges000
deleteSelectedNodes000
deleteWindow000
demoSimpleGraph000
displayGraph000
dockPanel000
eda000
eda.names000
existing.CytoscapeWindow000
fitContent000
fitSelectedContent000
floatPanel000
getAdjacentEdgeNames000
getAllEdgeAttributes000
getAllEdges000
getAllNodeAttributes000
getAllNodes0.000.020.02
getArrowShapes000
getAttributeClassNames000
getCenter000
getDefaultBackgroundColor000
getDefaultEdgeReverseSelectionColor000
getDefaultEdgeSelectionColor000
getDefaultNodeReverseSelectionColor000
getDefaultNodeSelectionColor000
getDirectlyModifiableVisualProperties000
getEdgeAttribute000
getEdgeAttributeNames000
getEdgeCount000
getFirstNeighbors000
getGraph000
getGraphFromCyWindow000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType000
getLayoutPropertyValue000
getLineStyles000
getNodeAttribute000
getNodeAttributeNames000
getNodeCount000
getNodePosition000
getNodeShapes000
getNodeSize000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes000
getViewCoordinates000
getVisualStyleNames000
getWindowCount000
getWindowID000
getWindowList000
getZoom000
hideAllPanels000
hideNodes000
hidePanel000
hideSelectedEdges000
hideSelectedNodes000
initEdgeAttribute000
initNodeAttribute000
invertEdgeSelection000
invertNodeSelection000
layoutNetwork0.020.000.01
lockNodeDimensions000
makeRandomGraph000
makeSimpleGraph000
noa000
noa.names000
ping000
pluginVersion000
predictTimeToDisplayGraph000
raiseWindow000
redraw000
restoreLayout000
saveImage0.020.000.02
saveLayout000
saveNetwork000
selectEdges000
selectFirstNeighborsOfSelectedNodes000
selectNodes000
sendEdges000
sendNodes000
setCenter000
setDefaultBackgroundColor000
setDefaultEdgeColor000
setDefaultEdgeFontSize000
setDefaultEdgeLineWidth000
setDefaultEdgeReverseSelectionColor000
setDefaultEdgeSelectionColor000
setDefaultEdgeSourceArrowColor000
setDefaultEdgeTargetArrowColor000
setDefaultNodeBorderColor000
setDefaultNodeBorderWidth000
setDefaultNodeColor000
setDefaultNodeFontSize000
setDefaultNodeLabelColor000
setDefaultNodeReverseSelectionColor000
setDefaultNodeSelectionColor000
setDefaultNodeShape0.020.000.02
setDefaultNodeSize000
setEdgeAttributes000
setEdgeAttributesDirect000
setEdgeColorDirect000
setEdgeColorRule000
setEdgeFontSizeDirect000
setEdgeLabelColorDirect000
setEdgeLabelDirect000
setEdgeLabelOpacityDirect000
setEdgeLabelRule000
setEdgeLineStyleDirect000
setEdgeLineStyleRule000
setEdgeLineWidthDirect000
setEdgeLineWidthRule000
setEdgeOpacityDirect000
setEdgeOpacityRule000
setEdgeSourceArrowColorDirect000
setEdgeSourceArrowColorRule000
setEdgeSourceArrowOpacityDirect000
setEdgeSourceArrowRule000
setEdgeSourceArrowShapeDirect000
setEdgeTargetArrowColorDirect0.010.000.02
setEdgeTargetArrowColorRule000
setEdgeTargetArrowOpacityDirect000
setEdgeTargetArrowRule000
setEdgeTargetArrowShapeDirect000
setEdgeTooltipDirect000
setEdgeTooltipRule000
setGraph000
setLayoutProperties000
setNodeAttributes000
setNodeAttributesDirect000
setNodeBorderColorDirect000
setNodeBorderColorRule000
setNodeBorderOpacityDirect000
setNodeBorderWidthDirect000
setNodeBorderWidthRule000
setNodeColorDirect000
setNodeColorRule000
setNodeFillOpacityDirect000
setNodeFontSizeDirect000
setNodeHeightDirect000
setNodeImageDirect000
setNodeLabelColorDirect000
setNodeLabelDirect000
setNodeLabelOpacityDirect000
setNodeLabelRule000
setNodeOpacityDirect000
setNodeOpacityRule000
setNodePosition000
setNodeShapeDirect000
setNodeShapeRule000
setNodeSizeDirect000
setNodeSizeRule000
setNodeTooltipRule000
setNodeWidthDirect000
setTooltipDismissDelay000
setTooltipInitialDelay000
setVisualStyle000
setWindowSize000
setZoom000
showGraphicsDetails000
unhideAll000

RCy3.Rcheck/examples_x64/RCy3-Ex.timings:

nameusersystemelapsed
CytoscapeConnection000
CytoscapeConnectionClass-class000
CytoscapeWindow000
CytoscapeWindowClass-class000
addCyEdge000
addCyNode000
addGraphToGraph000
clearSelection000
copyVisualStyle000
createWindow000
createWindowFromSelection000
cy2.edge.names000
cyPlot000
deleteAllWindows000
deleteEdgeAttribute000
deleteNodeAttribute0.020.000.02
deleteSelectedEdges000
deleteSelectedNodes000
deleteWindow000
demoSimpleGraph000
displayGraph000
dockPanel000
eda000
eda.names000
existing.CytoscapeWindow000
fitContent000
fitSelectedContent0.010.000.01
floatPanel000
getAdjacentEdgeNames000
getAllEdgeAttributes000
getAllEdges000
getAllNodeAttributes000
getAllNodes000
getArrowShapes000
getAttributeClassNames000
getCenter000
getDefaultBackgroundColor000
getDefaultEdgeReverseSelectionColor000
getDefaultEdgeSelectionColor000
getDefaultNodeReverseSelectionColor000
getDefaultNodeSelectionColor000
getDirectlyModifiableVisualProperties000
getEdgeAttribute000
getEdgeAttributeNames000
getEdgeCount000
getFirstNeighbors000
getGraph000
getGraphFromCyWindow000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType000
getLayoutPropertyValue000
getLineStyles000
getNodeAttribute000
getNodeAttributeNames000
getNodeCount000
getNodePosition000
getNodeShapes000
getNodeSize000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes000
getViewCoordinates000
getVisualStyleNames000
getWindowCount000
getWindowID000
getWindowList000
getZoom000
hideAllPanels000
hideNodes000
hidePanel0.000.020.02
hideSelectedEdges000
hideSelectedNodes000
initEdgeAttribute000
initNodeAttribute000
invertEdgeSelection000
invertNodeSelection000
layoutNetwork000
lockNodeDimensions000
makeRandomGraph000
makeSimpleGraph000
noa000
noa.names000
ping000
pluginVersion000
predictTimeToDisplayGraph000
raiseWindow000
redraw000
restoreLayout000
saveImage000
saveLayout000
saveNetwork000
selectEdges000
selectFirstNeighborsOfSelectedNodes000
selectNodes000
sendEdges000
sendNodes000
setCenter000
setDefaultBackgroundColor000
setDefaultEdgeColor000
setDefaultEdgeFontSize000
setDefaultEdgeLineWidth000
setDefaultEdgeReverseSelectionColor000
setDefaultEdgeSelectionColor000
setDefaultEdgeSourceArrowColor0.020.000.01
setDefaultEdgeTargetArrowColor000
setDefaultNodeBorderColor000
setDefaultNodeBorderWidth000
setDefaultNodeColor000
setDefaultNodeFontSize000
setDefaultNodeLabelColor000
setDefaultNodeReverseSelectionColor000
setDefaultNodeSelectionColor000
setDefaultNodeShape000
setDefaultNodeSize000
setEdgeAttributes000
setEdgeAttributesDirect000
setEdgeColorDirect000
setEdgeColorRule000
setEdgeFontSizeDirect000
setEdgeLabelColorDirect000
setEdgeLabelDirect000
setEdgeLabelOpacityDirect000
setEdgeLabelRule000
setEdgeLineStyleDirect000
setEdgeLineStyleRule0.020.000.02
setEdgeLineWidthDirect000
setEdgeLineWidthRule000
setEdgeOpacityDirect000
setEdgeOpacityRule000
setEdgeSourceArrowColorDirect000
setEdgeSourceArrowColorRule000
setEdgeSourceArrowOpacityDirect000
setEdgeSourceArrowRule000
setEdgeSourceArrowShapeDirect000
setEdgeTargetArrowColorDirect0.010.000.01
setEdgeTargetArrowColorRule000
setEdgeTargetArrowOpacityDirect000
setEdgeTargetArrowRule000
setEdgeTargetArrowShapeDirect000
setEdgeTooltipDirect000
setEdgeTooltipRule000
setGraph000
setLayoutProperties000
setNodeAttributes000
setNodeAttributesDirect000
setNodeBorderColorDirect000
setNodeBorderColorRule000
setNodeBorderOpacityDirect000
setNodeBorderWidthDirect000
setNodeBorderWidthRule000
setNodeColorDirect000
setNodeColorRule000
setNodeFillOpacityDirect000
setNodeFontSizeDirect000
setNodeHeightDirect000
setNodeImageDirect000
setNodeLabelColorDirect0.000.010.01
setNodeLabelDirect000
setNodeLabelOpacityDirect000
setNodeLabelRule000
setNodeOpacityDirect000
setNodeOpacityRule000
setNodePosition000
setNodeShapeDirect000
setNodeShapeRule000
setNodeSizeDirect000
setNodeSizeRule000
setNodeTooltipRule0.010.000.02
setNodeWidthDirect000
setTooltipDismissDelay000
setTooltipInitialDelay000
setVisualStyle000
setWindowSize000
setZoom000
showGraphicsDetails000
unhideAll000