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This page was generated on 2021-06-18 14:06:56 -0400 (Fri, 18 Jun 2021).

CHECK results for RCy3 on machv2

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.

raw results

Package 1526/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.12.3  (landing page)
Alex Pico
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/RCy3
Branch: RELEASE_3_13
Last Commit: 47168d0
Last Changed Date: 2021-06-15 21:28:25 -0400 (Tue, 15 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: RCy3
Version: 2.12.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCy3_2.12.3.tar.gz
StartedAt: 2021-06-17 22:41:56 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 22:44:04 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 128.5 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCy3_2.12.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/RCy3.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.12.3’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
  .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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/RCy3.Rcheck/00check.log’
for details.



Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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 
  0.242   0.059   0.280 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
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addAnnotationText0.0000.0010.000
addCyEdges0.0000.0000.001
addCyNodes0.0000.0000.001
analyzeNetwork000
applyFilter0.0010.0000.000
bundleEdges0.0000.0010.001
checkNotebookIsRunning0.0000.0000.001
checkRunningRemote0.0000.0000.001
clearEdgeBends000
clearEdgePropertyBypass0.0000.0000.001
clearNetworkCenterBypass0.0000.0010.000
clearNetworkPropertyBypass000
clearNetworkZoomBypass000
clearNodeOpacityBypass0.0000.0010.000
clearNodePropertyBypass0.0000.0000.001
clearSelection000
cloneNetwork0.0000.0010.000
closeSession000
collapseGroup000
commandEcho000
commandOpenDialog0.0000.0000.001
commandPause000
commandQuit000
commandRunFile000
commandSleep000
commandsAPI000
commandsGET0.0000.0010.000
commandsHelp0.0010.0000.000
commandsPOST000
commandsRun000
copyVisualStyle000
createColumnFilter000
createCompositeFilter0.0000.0000.001
createDegreeFilter0.0000.0010.000
createGraphFromNetwork000
createGroup0.0000.0010.000
createGroupByColumn000
createIgraphFromNetwork0.0000.0010.000
createNetworkFromDataFrames0.0010.0000.001
createNetworkFromGraph0.0010.0000.000
createNetworkFromIgraph0.0000.0000.001
createSubnetwork0.0000.0010.000
createVisualStyle000
cybrowserClose0.0000.0000.001
cybrowserDialog0.0000.0010.000
cybrowserHide000
cybrowserList0.0000.0010.000
cybrowserSend0.0000.0000.001
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE0.0000.0000.001
cyrestGET0.0010.0000.000
cyrestPOST000
cyrestPUT000
cytoscapeApiVersions0.0010.0000.001
cytoscapeFreeMemory000
cytoscapeMemoryStatus0.0000.0000.001
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo0.0010.0010.000
deleteAllNetworks0.0010.0000.001
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup000
deleteNetwork000
deleteSelectedEdges0.0010.0000.000
deleteSelectedNodes000
deleteSelfLoops0.0000.0010.000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle0.0000.0000.001
diffusionAdvanced0.0000.0000.001
diffusionBasic0.0000.0000.001
disableApp0.0000.0000.001
doInitializeSandbox000
doRequestRemote000
doSetSandbox000
dockPanel000
dot-getDefaultSandbox0.0010.0000.000
dot-getRequester0.0000.0010.000
enableApp000
expandGroup000
exportFilters000
exportImage000
exportNetwork000
exportNetworkToNDEx000
exportVisualStyles000
findRemoteCytoscape000
fitContent000
floatPanel000
getAbsSandboxPath000
getAllEdges0.0000.0010.000
getAllNodes0.0000.0000.001
getAllStyleMappings0.0010.0000.001
getAnnotationList0.0000.0000.001
getAppInformation0.0000.0000.001
getAppStatus000
getAppUpdates000
getArrowShapes000
getAvailableApps000
getBackgroundColorDefault000
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList0.0000.0010.000
getCollectionName000
getCollectionNetworks000
getCollectionSuid000
getCurrentSandbox000
getCurrentSandboxName000
getCurrentSandboxPath000
getCurrentStyle000
getDefaultSandbox0.0000.0000.001
getDefaultSandboxPath0.0000.0000.001
getDisabledApps0.0000.0000.001
getEdgeColor0.0000.0000.001
getEdgeCount0.0000.0010.000
getEdgeInfo000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty000
getEdgeSelectionColorDefault0.0000.0010.000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors0.0010.0000.000
getGroupInfo000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping0.0000.0010.000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType000
getLayoutPropertyValue000
getLineStyles0.0000.0010.001
getNetworkCenter0.0000.0000.001
getNetworkCount0.0000.0000.001
getNetworkList000
getNetworkNDExId0.0010.0000.000
getNetworkName000
getNetworkProperty0.0000.0000.001
getNetworkSuid0.0000.0000.001
getNetworkViewSuid0.0000.0000.001
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount000
getNodeHeight0.0000.0000.001
getNodePosition000
getNodeProperty0.0010.0000.000
getNodeSelectionColorDefault0.0010.0010.001
getNodeShapes000
getNodeSize000
getNodeWidth0.0000.0010.001
getNotebookIsRunning000
getSandboxReinitialize0.0000.0010.001
getSelectedEdgeCount0.0000.0000.001
getSelectedEdges0.0010.0000.001
getSelectedNodeCount000
getSelectedNodes0.0000.0010.001
getStyleDependencies0.0000.0000.001
getStyleMapping000
getTableColumnNames0.0000.0010.000
getTableColumnTypes0.0000.0000.001
getTableColumns0.0010.0000.000
getTableValue000
getUninstalledApps000
getVisualPropertyDefault0.0000.0000.001
getVisualPropertyNames0.0000.0010.000
getVisualStyleNames0.0000.0000.001
hideAllPanels0.0010.0000.000
hideEdges000
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hidePanel000
hideSelectedEdges000
hideSelectedNodes0.0010.0000.000
importFilters000
importNetworkFromFile0.0000.0000.001
importNetworkFromNDEx000
importVisualStyles0.0000.0010.000
installApp0.0000.0000.001
invertEdgeSelection000
invertNodeSelection0.0000.0000.001
layoutCopycat000
layoutNetwork000
listGroups000
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makeSimpleIgraph0.0160.0020.017
mapTableColumn000
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matchArrowColorToEdge000
mergeNetworks0.0010.0010.000
openAppStore0.0010.0000.000
openSession0.0010.0000.001
paletteColorBrewerAccent0.0090.0000.009
paletteColorBrewerBlues0.0000.0000.001
paletteColorBrewerBrBG0.0000.0010.001
paletteColorBrewerBuGn0.0000.0000.001
paletteColorBrewerBuPu000
paletteColorBrewerDark2000
paletteColorBrewerGnBu000
paletteColorBrewerGreens0.0000.0010.001
paletteColorBrewerGreys000
paletteColorBrewerOrRd0.0000.0010.000
paletteColorBrewerOranges000
paletteColorBrewerPRGn000
paletteColorBrewerPaired0.0000.0000.001
paletteColorBrewerPastel10.0000.0000.001
paletteColorBrewerPastel2000
paletteColorBrewerPiYG000
paletteColorBrewerPuBu000
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr0.0000.0000.001
paletteColorBrewerPuRd0.0000.0010.000
paletteColorBrewerPurples000
paletteColorBrewerRdBu0.0000.0000.001
paletteColorBrewerRdPu0.0000.0010.000
paletteColorBrewerRdYlBu000
paletteColorBrewerReds0.0000.0000.001
paletteColorBrewerSet1000
paletteColorBrewerSet2000
paletteColorBrewerSet30.0000.0010.001
paletteColorBrewerYlGn0.0000.0000.001
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr000
paletteColorBrewerYlOrRd000
paletteColorRandom0.0000.0000.001
removeNodeCustomGraphics000
renameNetwork0.0000.0000.001
renameTableColumn0.0000.0000.001
resetDefaultSandbox0.0010.0000.001
runningRemoteCheck0.0000.0010.001
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sandboxGetFrom000
sandboxInitializer000
sandboxRemove000
sandboxRemoveFile000
sandboxSendTo000
sandboxSet000
sandboxUrlTo000
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selectEdgesConnectingSelectedNodes0.0000.0000.001
selectFirstNeighbors000
selectNodes000
selectNodesConnectedBySelectedEdges000
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setCatchupFilterSecs0.0000.0010.000
setCatchupNetworkSecs0.0000.0000.001
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setCurrentSandbox0.0010.0000.001
setCurrentView0.0000.0000.001
setDefaultSandbox000
setDefaultSandboxPath000
setEdgeColorBypass0.0000.0010.000
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setEdgeFontSizeBypass000
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setEdgeFontSizeMapping000
setEdgeLabelBypass000
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setEdgeLabelColorMapping0.0010.0000.001
setEdgeLabelDefault000
setEdgeLabelMapping000
setEdgeLabelOpacityBypass0.0010.0000.000
setEdgeLabelOpacityDefault000
setEdgeLabelOpacityMapping0.0000.0010.001
setEdgeLineStyleBypass0.0000.0000.001
setEdgeLineStyleDefault0.0000.0000.001
setEdgeLineStyleMapping000
setEdgeLineWidthBypass000
setEdgeLineWidthDefault000
setEdgeLineWidthMapping0.0000.0010.000
setEdgeOpacityBypass000
setEdgeOpacityDefault000
setEdgeOpacityMapping0.0000.0010.000
setEdgePropertyBypass000
setEdgeSelectionColorDefault000
setEdgeSourceArrowColorBypass000
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass0.0000.0000.001
setEdgeSourceArrowShapeDefault000
setEdgeSourceArrowShapeMapping000
setEdgeTargetArrowColorBypass000
setEdgeTargetArrowColorDefault000
setEdgeTargetArrowColorMapping000
setEdgeTargetArrowMapping000
setEdgeTargetArrowShapeBypass0.0000.0000.001
setEdgeTargetArrowShapeDefault0.0000.0000.001
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setEdgeTooltipBypass000
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setModelPropagationSecs0.0010.0010.000
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