Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:05:44 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for RCy3 on nebbiolo2


To the developers/maintainers of the RCy3 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCy3.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1576/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.17.0  (landing page)
Alex Pico
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: master
git_last_commit: 49a28e6
git_last_commit_date: 2022-04-26 11:27:59 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RCy3
Version: 2.17.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings RCy3_2.17.0.tar.gz
StartedAt: 2022-06-23 21:25:21 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:26:20 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 59.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings RCy3_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/RCy3.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* 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 ‘2.17.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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
createNetworkFromDataFrames: no visible binding for global variable
  ‘SUID’
Undefined global functions or variables:
  SUID
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/RCy3.Rcheck/00check.log’
for details.



Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘RCy3’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCy3)

Tests output

RCy3.Rcheck/tests/runTests.Rout


R version 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # tests disabled as the Bioconductor build system no longer supports interactive sessions
> #require(RCy3) || stop("unable to load RCy3")
> #BiocGenerics:::testPackage('RCy3')
> 
> proc.time()
   user  system elapsed 
  0.157   0.025   0.166 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
AddToGroup000
RemoveFromGroup000
UpdateAnnotationBoundedText000
addAnnotationBoundedText000
addAnnotationImage000
addAnnotationShape0.0000.0000.001
addAnnotationText000
addCyEdges000
addCyNodes000
analyzeNetwork000
applyFilter000
bundleEdges000
checkNotebookIsRunning000
checkRunningRemote000
clearEdgeBends000
clearEdgePropertyBypass000
clearNetworkCenterBypass000
clearNetworkPropertyBypass000
clearNetworkZoomBypass000
clearNodeOpacityBypass000
clearNodePropertyBypass000
clearSelection000
cloneNetwork0.0010.0000.000
closeSession000
collapseGroup000
commandEcho000
commandOpenDialog000
commandPause000
commandQuit000
commandRunFile000
commandSleep0.0010.0000.000
commandsAPI000
commandsGET0.0000.0000.001
commandsHelp000
commandsPOST000
commandsRun000
copyVisualStyle000
createColumnFilter000
createCompositeFilter000
createDegreeFilter000
createGraphFromNetwork000
createGroup000
createGroupByColumn000
createIgraphFromNetwork0.0010.0000.000
createNetworkFromDataFrames000
createNetworkFromGraph0.0000.0000.001
createNetworkFromIgraph000
createSubnetwork000
createView000
createVisualStyle000
cybrowserClose000
cybrowserDialog0.0010.0000.000
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE000
cyrestGET000
cyrestPOST000
cyrestPUT000
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores000
cytoscapePing0.0000.0000.001
cytoscapeVersionInfo000
deleteAllNetworks000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup000
deleteNetwork000
deleteSelectedEdges000
deleteSelectedNodes0.0000.0000.001
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle000
diffusionAdvanced000
diffusionBasic000
disableApp000
doInitializeSandbox000
doRequestRemote000
doSetSandbox000
dockPanel000
dot-exportShowImage000
dot-getDefaultSandbox000
dot-getRequester000
enableApp000
expandGroup000
exportFilters0.0010.0000.000
exportImage000
exportNetwork0.0000.0000.001
exportNetworkToNDEx000
exportVisualStyles000
findRemoteCytoscape000
fitContent000
floatPanel000
getAbsSandboxPath000
getAllEdges000
getAllNodes0.0000.0000.001
getAllStyleMappings000
getAnnotationList000
getAppInformation000
getAppStatus000
getAppUpdates000
getArrowShapes0.0010.0000.000
getAvailableApps000
getBackgroundColorDefault0.0000.0000.001
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList000
getCollectionName000
getCollectionNetworks000
getCollectionSuid000
getCurrentSandbox000
getCurrentSandboxName000
getCurrentSandboxPath000
getCurrentStyle000
getDefaultSandbox000
getDefaultSandboxPath000
getDisabledApps000
getEdgeColor000
getEdgeCount000
getEdgeInfo000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo0.0010.0000.000
getInstalledApps000
getJupyterBridgeURL0.0000.0000.001
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType000
getLayoutPropertyValue000
getLineStyles000
getNetworkCenter000
getNetworkCount000
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid0.0000.0000.001
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount000
getNodeHeight000
getNodePosition000
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth000
getNotebookIsRunning000
getSandboxReinitialize0.0010.0000.000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes000
getStyleDependencies000
getStyleMapping000
getTableColumnNames000
getTableColumnTypes000
getTableColumns000
getTableValue000
getUninstalledApps000
getVisualPropertyDefault000
getVisualPropertyNames000
getVisualStyleNames000
groupAnnotation000
hideAllPanels000
hideEdges000
hideNodes000
hidePanel0.0010.0000.000
hideSelectedEdges000
hideSelectedNodes000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx000
importVisualStyles000
installApp000
invertEdgeSelection000
invertNodeSelection000
layoutCopycat000
layoutNetwork000
listGroups000
lockNodeDimensions0.0010.0000.000
makeSimpleGraph0.0510.0000.051
makeSimpleIgraph0.0440.0030.048
mapTableColumn000
mapVisualProperty0.0010.0010.000
matchArrowColorToEdge000
mergeNetworks000
notebookExportShowImage000
notebookShowImage000
openAppStore000
openSession000
paletteColorBrewerAccent0.0040.0000.005
paletteColorBrewerBlues000
paletteColorBrewerBrBG000
paletteColorBrewerBuGn000
paletteColorBrewerBuPu000
paletteColorBrewerDark2000
paletteColorBrewerGnBu0.0000.0000.001
paletteColorBrewerGreens000
paletteColorBrewerGreys0.0000.0000.001
paletteColorBrewerOrRd000
paletteColorBrewerOranges000
paletteColorBrewerPRGn000
paletteColorBrewerPaired000
paletteColorBrewerPastel1000
paletteColorBrewerPastel2000
paletteColorBrewerPiYG0.0010.0000.000
paletteColorBrewerPuBu000
paletteColorBrewerPuBuGn0.0010.0000.000
paletteColorBrewerPuOr000
paletteColorBrewerPuRd0.0010.0000.000
paletteColorBrewerPurples000
paletteColorBrewerRdBu000
paletteColorBrewerRdPu000
paletteColorBrewerRdYlBu000
paletteColorBrewerReds000
paletteColorBrewerSet10.0000.0000.001
paletteColorBrewerSet20.0000.0010.000
paletteColorBrewerSet30.0000.0000.001
paletteColorBrewerYlGn0.0000.0010.000
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr000
paletteColorBrewerYlOrRd000
paletteColorRandom000
removeNodeCustomGraphics0.0000.0000.001
renameNetwork000
renameTableColumn000
resetDefaultSandbox000
runningRemoteCheck000
sandboxGetFileInfo000
sandboxGetFrom000
sandboxInitializer000
sandboxRemove000
sandboxRemoveFile000
sandboxSendTo000
sandboxSet000
sandboxUrlTo000
saveSession000
selectAll000
selectAllEdges000
selectAllNodes000
selectEdges000
selectEdgesAdjacentToSelectedNodes000
selectEdgesConnectingSelectedNodes000
selectFirstNeighbors000
selectNodes000
selectNodesConnectedBySelectedEdges000
setBackgroundColorDefault000
setCatchupFilterSecs0.0000.0000.001
setCatchupNetworkSecs000
setCurrentNetwork000
setCurrentSandbox0.0010.0000.000
setCurrentView000
setDefaultSandbox0.0000.0000.001
setDefaultSandboxPath000
setEdgeColorBypass000
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setEdgeFontFaceBypass000
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setEdgeFontSizeBypass0.0000.0000.001
setEdgeFontSizeDefault000
setEdgeFontSizeMapping000
setEdgeLabelBypass000
setEdgeLabelColorBypass000
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setEdgeLabelColorMapping0.0010.0000.000
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setEdgeLabelMapping0.0000.0000.001
setEdgeLabelOpacityBypass000
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setEdgeLineWidthBypass000
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setEdgeLineWidthMapping0.0010.0000.000
setEdgeOpacityBypass000
setEdgeOpacityDefault0.0000.0000.001
setEdgeOpacityMapping000
setEdgePropertyBypass000
setEdgeSelectionColorDefault000
setEdgeSourceArrowColorBypass000
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass000
setEdgeSourceArrowShapeDefault000
setEdgeSourceArrowShapeMapping000
setEdgeTargetArrowColorBypass000
setEdgeTargetArrowColorDefault000
setEdgeTargetArrowColorMapping000
setEdgeTargetArrowMapping000
setEdgeTargetArrowShapeBypass000
setEdgeTargetArrowShapeDefault000
setEdgeTargetArrowShapeMapping000
setEdgeTooltipBypass000
setEdgeTooltipDefault000
setEdgeTooltipMapping000
setLayoutProperties000
setModelPropagationSecs000
setNetworkCenterBypass0.0000.0000.001
setNetworkPropertyBypass000
setNetworkZoomBypass000
setNodeBorderColorBypass000
setNodeBorderColorDefault000
setNodeBorderColorMapping000
setNodeBorderOpacityBypass0.0010.0000.000
setNodeBorderOpacityDefault000
setNodeBorderOpacityMapping0.0000.0000.001
setNodeBorderWidthBypass000
setNodeBorderWidthDefault000
setNodeBorderWidthMapping000
setNodeColorBypass000
setNodeColorDefault000
setNodeColorMapping000
setNodeComboOpacityMapping000
setNodeCustomBarChart000
setNodeCustomBoxChart000
setNodeCustomHeatMapChart000
setNodeCustomLineChart0.0000.0000.001
setNodeCustomLinearGradient000
setNodeCustomPieChart000
setNodeCustomPosition000
setNodeCustomRadialGradient000
setNodeCustomRingChart000
setNodeFillOpacityBypass000
setNodeFillOpacityDefault000
setNodeFillOpacityMapping000
setNodeFontFaceBypass000
setNodeFontFaceDefault000
setNodeFontFaceMapping000
setNodeFontSizeBypass000
setNodeFontSizeDefault000
setNodeFontSizeMapping000
setNodeHeightBypass000
setNodeHeightDefault000
setNodeHeightMapping000
setNodeLabelBypass000
setNodeLabelColorBypass0.0000.0000.001
setNodeLabelColorDefault000
setNodeLabelColorMapping000
setNodeLabelDefault000
setNodeLabelMapping000
setNodeLabelOpacityBypass000
setNodeLabelOpacityDefault000
setNodeLabelOpacityMapping000
setNodeOpacityBypass000
setNodePropertyBypass0.0010.0000.000
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setNodeShapeBypass0.0000.0000.001
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setNodeTooltipBypass000
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setNodeWidthBypass0.0010.0000.000
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setNodeWidthMapping0.0000.0000.001
setNotebookIsRunning000
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setVisualPropertyDefault000
setVisualStyle000
syncNodeCustomGraphicsSize000
toggleGraphicsDetails000
ungroupAnnotation000
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unhideNodes0.0000.0000.001
uninstallApp000
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updateAnnotationShape000
updateAnnotationText000
updateApp000
updateGroupAnnotation000
updateNetworkInNDEx000
updateStyleDefaults000
updateStyleMapping000