Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-30 15:05:38 -0400 (Fri, 30 Jul 2021).

CHECK results for RCy3 on nebbiolo1

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: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 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  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

Summary

Package: RCy3
Version: 2.12.3
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_2.12.3.tar.gz
StartedAt: 2021-07-29 11:18:57 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 11:20:15 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 77.9 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_2.12.3.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 ‘2.12.3’
* 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:
  .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 
  0.160   0.031   0.175 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
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addAnnotationText000
addCyEdges0.0010.0000.001
addCyNodes000
analyzeNetwork000
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checkNotebookIsRunning000
checkRunningRemote0.0010.0000.000
clearEdgeBends000
clearEdgePropertyBypass000
clearNetworkCenterBypass000
clearNetworkPropertyBypass000
clearNetworkZoomBypass000
clearNodeOpacityBypass0.0000.0010.000
clearNodePropertyBypass000
clearSelection0.0000.0000.001
cloneNetwork0.0000.0010.000
closeSession000
collapseGroup0.0000.0000.001
commandEcho000
commandOpenDialog000
commandPause000
commandQuit000
commandRunFile000
commandSleep000
commandsAPI000
commandsGET0.0010.0000.001
commandsHelp000
commandsPOST000
commandsRun0.0010.0000.001
copyVisualStyle000
createColumnFilter000
createCompositeFilter0.0010.0000.001
createDegreeFilter000
createGraphFromNetwork000
createGroup0.0010.0000.001
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromDataFrames0.0000.0000.001
createNetworkFromGraph000
createNetworkFromIgraph000
createSubnetwork000
createVisualStyle000
cybrowserClose000
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE0.0010.0000.000
cyrestGET0.0000.0010.000
cyrestPOST000
cyrestPUT0.0000.0000.001
cytoscapeApiVersions0.0000.0010.000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup0.0000.0000.001
deleteNetwork000
deleteSelectedEdges000
deleteSelectedNodes000
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle0.0010.0000.001
diffusionAdvanced000
diffusionBasic000
disableApp0.0000.0000.001
doInitializeSandbox0.0000.0010.000
doRequestRemote000
doSetSandbox000
dockPanel0.0000.0010.000
dot-getDefaultSandbox000
dot-getRequester0.0000.0000.001
enableApp0.0000.0010.000
expandGroup000
exportFilters0.0000.0000.001
exportImage0.0000.0010.000
exportNetwork000
exportNetworkToNDEx0.0000.0000.001
exportVisualStyles0.0000.0010.000
findRemoteCytoscape000
fitContent0.0000.0000.001
floatPanel0.0000.0010.000
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getEdgeInfo0.0010.0000.000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty0.0010.0000.001
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames0.0000.0000.001
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getLayoutPropertyType000
getLayoutPropertyValue0.0000.0000.001
getLineStyles0.0000.0010.000
getNetworkCenter000
getNetworkCount0.0010.0000.000
getNetworkList000
getNetworkNDExId000
getNetworkName0.0010.0000.001
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid0.0010.0000.001
getNetworkViews000
getNetworkZoom000
getNodeColor0.0010.0000.001
getNodeCount000
getNodeHeight000
getNodePosition0.0010.0000.001
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes0.0010.0000.001
getNodeSize000
getNodeWidth000
getNotebookIsRunning0.0010.0000.001
getSandboxReinitialize000
getSelectedEdgeCount000
getSelectedEdges0.0010.0000.001
getSelectedNodeCount000
getSelectedNodes000
getStyleDependencies0.0010.0000.001
getStyleMapping000
getTableColumnNames000
getTableColumnTypes0.0010.0000.001
getTableColumns000
getTableValue000
getUninstalledApps0.0000.0000.001
getVisualPropertyDefault000
getVisualPropertyNames000
getVisualStyleNames0.0000.0000.001
hideAllPanels000
hideEdges000
hideNodes0.0010.0000.001
hidePanel000
hideSelectedEdges000
hideSelectedNodes0.0010.0000.001
importFilters000
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importNetworkFromNDEx0.0000.0000.001
importVisualStyles000
installApp000
invertEdgeSelection0.0000.0000.001
invertNodeSelection000
layoutCopycat0.0000.0010.000
layoutNetwork000
listGroups000
lockNodeDimensions0.0000.0010.000
makeSimpleGraph0.0490.0050.053
makeSimpleIgraph0.020.000.02
mapTableColumn000
mapVisualProperty000
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mergeNetworks000
openAppStore000
openSession0.0010.0000.000
paletteColorBrewerAccent0.0050.0000.005
paletteColorBrewerBlues000
paletteColorBrewerBrBG000
paletteColorBrewerBuGn000
paletteColorBrewerBuPu000
paletteColorBrewerDark2000
paletteColorBrewerGnBu0.0000.0000.001
paletteColorBrewerGreens0.0000.0000.001
paletteColorBrewerGreys0.0000.0010.000
paletteColorBrewerOrRd0.0000.0010.000
paletteColorBrewerOranges000
paletteColorBrewerPRGn000
paletteColorBrewerPaired0.0010.0000.000
paletteColorBrewerPastel10.0010.0000.001
paletteColorBrewerPastel2000
paletteColorBrewerPiYG000
paletteColorBrewerPuBu000
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr000
paletteColorBrewerPuRd0.0000.0000.001
paletteColorBrewerPurples0.0000.0000.001
paletteColorBrewerRdBu0.0000.0000.001
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paletteColorBrewerReds000
paletteColorBrewerSet1000
paletteColorBrewerSet20.0010.0000.001
paletteColorBrewerSet3000
paletteColorBrewerYlGn000
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr0.0010.0000.000
paletteColorBrewerYlOrRd0.0010.0000.001
paletteColorRandom0.0010.0000.001
removeNodeCustomGraphics000
renameNetwork000
renameTableColumn000
resetDefaultSandbox000
runningRemoteCheck000
sandboxGetFileInfo0.0000.0000.001
sandboxGetFrom000
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sandboxRemove0.0000.0000.001
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setEdgeSourceArrowColorBypass0.0000.0010.000
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping000
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setModelPropagationSecs000
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