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CHECK results for RCy3 on nebbiolo1

This page was generated on 2021-06-14 14:04:59 -0400 (Mon, 14 Jun 2021).

Package 1526/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.12.2  (landing page)
Alex Pico
Snapshot Date: 2021-06-13 06:50:09 -0400 (Sun, 13 Jun 2021)
URL: https://git.bioconductor.org/packages/RCy3
Branch: RELEASE_3_13
Last Commit: 6fe1644
Last Changed Date: 2021-06-01 15:32:14 -0400 (Tue, 01 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

Summary

Package: RCy3
Version: 2.12.2
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RCy3_2.12.2.tar.gz
StartedAt: 2021-06-13 13:14:47 -0400 (Sun, 13 Jun 2021)
EndedAt: 2021-06-13 13:16:08 -0400 (Sun, 13 Jun 2021)
EllapsedTime: 80.6 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RCy3_2.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RCy3.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘2.12.2’
* 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 ... 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
.edgeNameToEdgeSUID: no visible binding for global variable ‘SUID’
.nodeNameToNodeSUID: no visible binding for global variable ‘SUID’
commandsGET: no visible binding for global variable ‘requester’
commandsHelp: no visible binding for global variable ‘requester’
commandsPOST: no visible binding for global variable ‘requester’
createNetworkFromDataFrames: no visible binding for global variable
  ‘SUID’
cyrestDELETE: no visible binding for global variable ‘requester’
cyrestGET: no visible binding for global variable ‘requester’
cyrestPOST: no visible binding for global variable ‘requester’
cyrestPUT: no visible binding for global variable ‘requester’
paletteColorRandom: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  SUID requester rgb
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
* 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-3.13-bioc/meat/RCy3.Rcheck/00check.log’
for details.



Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 
  0.149   0.029   0.162 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
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addAnnotationText0.0000.0000.001
addCyEdges000
addCyNodes000
analyzeNetwork000
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bundleEdges0.0000.0010.000
checkNotebookIsRunning000
checkRunningRemote0.0000.0000.001
clearEdgeBends0.0010.0000.000
clearEdgePropertyBypass000
clearNetworkCenterBypass000
clearNetworkPropertyBypass000
clearNetworkZoomBypass0.0010.0000.000
clearNodeOpacityBypass000
clearNodePropertyBypass0.0000.0000.001
clearSelection0.0010.0000.000
cloneNetwork000
closeSession000
collapseGroup0.0000.0010.000
commandEcho000
commandOpenDialog0.0000.0000.001
commandPause000
commandQuit000
commandRunFile000
commandSleep000
commandsAPI0.0000.0010.000
commandsGET000
commandsHelp0.0000.0000.001
commandsPOST0.0000.0000.001
commandsRun0.0000.0000.001
copyVisualStyle000
createColumnFilter0.0010.0000.000
createCompositeFilter000
createDegreeFilter0.0000.0000.001
createGraphFromNetwork000
createGroup000
createGroupByColumn0.0000.0000.001
createIgraphFromNetwork0.0000.0010.000
createNetworkFromDataFrames000
createNetworkFromGraph000
createNetworkFromIgraph0.0000.0000.001
createSubnetwork0.0010.0000.000
createVisualStyle000
cybrowserClose000
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE000
cyrestGET000
cyrestPOST000
cyrestPUT0.0000.0000.001
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores0.0000.0000.001
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup000
deleteNetwork0.0010.0000.000
deleteSelectedEdges000
deleteSelectedNodes000
deleteSelfLoops0.0010.0000.000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle0.0000.0000.001
diffusionAdvanced000
diffusionBasic000
disableApp000
doInitializeSandbox0.0010.0000.000
doRequestRemote000
doSetSandbox000
dockPanel0.0000.0000.001
dot-getDefaultSandbox0.0000.0010.000
dot-getRequester000
enableApp0.0000.0000.001
expandGroup0.0000.0010.000
exportFilters000
exportImage0.0000.0000.001
exportNetwork000
exportNetworkToNDEx000
exportVisualStyles0.0000.0000.001
findRemoteCytoscape000
fitContent000
floatPanel000
getAbsSandboxPath000
getAllEdges000
getAllNodes0.0010.0000.000
getAllStyleMappings000
getAnnotationList000
getAppInformation0.0010.0000.000
getAppStatus000
getAppUpdates0.0000.0000.001
getArrowShapes0.0010.0000.000
getAvailableApps000
getBackgroundColorDefault0.0000.0000.001
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList0.0000.0000.001
getCollectionName000
getCollectionNetworks000
getCollectionSuid0.0010.0000.000
getCurrentSandbox000
getCurrentSandboxName0.0000.0010.000
getCurrentSandboxPath000
getCurrentStyle0.0000.0000.001
getDefaultSandbox000
getDefaultSandboxPath000
getDisabledApps0.0000.0000.001
getEdgeColor0.0000.0010.000
getEdgeCount000
getEdgeInfo000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo000
getInstalledApps000
getJupyterBridgeURL0.0000.0010.000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames0.0000.0010.000
getLayoutPropertyType000
getLayoutPropertyValue0.0000.0000.001
getLineStyles000
getNetworkCenter000
getNetworkCount0.0010.0000.001
getNetworkList000
getNetworkNDExId000
getNetworkName0.0010.0000.000
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid0.0010.0000.000
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount000
getNodeHeight000
getNodePosition000
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth000
getNotebookIsRunning000
getSandboxReinitialize0.0000.0000.001
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount0.0000.0000.001
getSelectedNodes000
getStyleDependencies000
getStyleMapping0.0000.0000.001
getTableColumnNames0.0010.0000.000
getTableColumnTypes000
getTableColumns000
getTableValue0.0000.0010.000
getUninstalledApps000
getVisualPropertyDefault000
getVisualPropertyNames000
getVisualStyleNames000
hideAllPanels000
hideEdges0.0010.0000.000
hideNodes000
hidePanel000
hideSelectedEdges0.0010.0000.000
hideSelectedNodes000
importFilters0.0000.0000.001
importNetworkFromFile0.0000.0010.000
importNetworkFromNDEx000
importVisualStyles0.0000.0000.001
installApp0.0000.0010.000
invertEdgeSelection000
invertNodeSelection000
layoutCopycat000
layoutNetwork0.0010.0000.000
listGroups000
lockNodeDimensions000
makeSimpleGraph0.0770.0000.077
makeSimpleIgraph0.0160.0000.017
mapTableColumn0.0000.0000.001
mapVisualProperty000
matchArrowColorToEdge000
mergeNetworks000
openAppStore000
openSession000
paletteColorBrewerAccent0.0050.0000.004
paletteColorBrewerBlues0.0010.0000.000
paletteColorBrewerBrBG000
paletteColorBrewerBuGn000
paletteColorBrewerBuPu0.0000.0000.001
paletteColorBrewerDark2000
paletteColorBrewerGnBu0.0010.0010.000
paletteColorBrewerGreens0.0000.0010.000
paletteColorBrewerGreys000
paletteColorBrewerOrRd0.0000.0000.001
paletteColorBrewerOranges0.0000.0000.001
paletteColorBrewerPRGn0.0000.0010.000
paletteColorBrewerPaired0.0000.0010.000
paletteColorBrewerPastel1000
paletteColorBrewerPastel2000
paletteColorBrewerPiYG0.0000.0000.001
paletteColorBrewerPuBu0.0000.0000.001
paletteColorBrewerPuBuGn0.0000.0000.001
paletteColorBrewerPuOr0.0000.0010.000
paletteColorBrewerPuRd000
paletteColorBrewerPurples000
paletteColorBrewerRdBu0.0000.0000.001
paletteColorBrewerRdPu0.0000.0000.001
paletteColorBrewerRdYlBu000
paletteColorBrewerReds0.0010.0000.000
paletteColorBrewerSet1000
paletteColorBrewerSet20.0000.0000.001
paletteColorBrewerSet3000
paletteColorBrewerYlGn0.0010.0000.000
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr0.0000.0000.001
paletteColorBrewerYlOrRd0.0000.0000.001
paletteColorRandom000
removeNodeCustomGraphics0.0010.0000.000
renameNetwork000
renameTableColumn000
resetDefaultSandbox000
runningRemoteCheck0.0000.0000.001
sandboxGetFileInfo000
sandboxGetFrom000
sandboxInitializer000
sandboxRemove0.0010.0000.000
sandboxRemoveFile0.0000.0000.001
sandboxSendTo0.0000.0010.000
sandboxSet000
sandboxUrlTo0.0000.0000.001
saveSession0.0000.0010.000
selectAllEdges000
selectAllNodes000
selectEdges000
selectEdgesAdjacentToSelectedNodes000
selectEdgesConnectingSelectedNodes000
selectFirstNeighbors000
selectNodes0.0000.0000.001
selectNodesConnectedBySelectedEdges000
setBackgroundColorDefault000
setCatchupFilterSecs0.0000.0000.001
setCatchupNetworkSecs000
setCurrentNetwork0.0010.0000.000
setCurrentSandbox000
setCurrentView000
setDefaultSandbox000
setDefaultSandboxPath0.0000.0000.001
setEdgeColorBypass000
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setEdgeColorMapping0.0000.0000.001
setEdgeFontFaceBypass0.0000.0010.000
setEdgeFontFaceDefault000
setEdgeFontFaceMapping000
setEdgeFontSizeBypass0.0010.0000.000
setEdgeFontSizeDefault000
setEdgeFontSizeMapping000
setEdgeLabelBypass000
setEdgeLabelColorBypass000
setEdgeLabelColorDefault0.0010.0000.000
setEdgeLabelColorMapping000
setEdgeLabelDefault000
setEdgeLabelMapping000
setEdgeLabelOpacityBypass0.0000.0000.001
setEdgeLabelOpacityDefault0.0000.0010.000
setEdgeLabelOpacityMapping000
setEdgeLineStyleBypass0.0000.0000.001
setEdgeLineStyleDefault000
setEdgeLineStyleMapping000
setEdgeLineWidthBypass000
setEdgeLineWidthDefault0.0010.0000.000
setEdgeLineWidthMapping0.0000.0000.001
setEdgeOpacityBypass0.0000.0010.000
setEdgeOpacityDefault000
setEdgeOpacityMapping0.0000.0000.001
setEdgePropertyBypass000
setEdgeSelectionColorDefault000
setEdgeSourceArrowColorBypass000
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping0.0000.0000.001
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass000
setEdgeSourceArrowShapeDefault000
setEdgeSourceArrowShapeMapping0.0010.0000.000
setEdgeTargetArrowColorBypass000
setEdgeTargetArrowColorDefault0.0000.0010.000
setEdgeTargetArrowColorMapping000
setEdgeTargetArrowMapping0.0000.0000.001
setEdgeTargetArrowShapeBypass000
setEdgeTargetArrowShapeDefault000
setEdgeTargetArrowShapeMapping000
setEdgeTooltipBypass000
setEdgeTooltipDefault000
setEdgeTooltipMapping000
setLayoutProperties000
setModelPropagationSecs0.0000.0000.001
setNetworkCenterBypass000
setNetworkPropertyBypass000
setNetworkZoomBypass0.0000.0000.001
setNodeBorderColorBypass000
setNodeBorderColorDefault000
setNodeBorderColorMapping000
setNodeBorderOpacityBypass0.0010.0000.000
setNodeBorderOpacityDefault000
setNodeBorderOpacityMapping000
setNodeBorderWidthBypass000
setNodeBorderWidthDefault000
setNodeBorderWidthMapping0.0000.0010.000
setNodeColorBypass000
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