Back to Build/check report for BioC 3.15
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This page was generated on 2022-06-27 11:10:05 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 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? 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 1595/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.16.0  (landing page)
Alex Pico
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: RELEASE_3_15
git_last_commit: 9488419
git_last_commit_date: 2022-04-26 11:27:59 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RCy3
Version: 2.16.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RCy3_2.16.0.tar.gz
StartedAt: 2022-06-26 21:29:25 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 21:30:28 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 62.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RCy3_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RCy3.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.16.0’
* 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-3.15-bioc/meat/RCy3.Rcheck/00check.log’
for details.



Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 (2022-04-22) -- "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 
  0.204   0.026   0.217 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

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analyzeNetwork000
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checkNotebookIsRunning000
checkRunningRemote000
clearEdgeBends000
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clearNetworkCenterBypass000
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clearNetworkZoomBypass0.0000.0000.001
clearNodeOpacityBypass000
clearNodePropertyBypass000
clearSelection000
cloneNetwork000
closeSession000
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commandEcho000
commandOpenDialog0.0000.0000.001
commandPause000
commandQuit000
commandRunFile0.0000.0000.001
commandSleep0.0010.0000.000
commandsAPI000
commandsGET000
commandsHelp000
commandsPOST000
commandsRun000
copyVisualStyle000
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createCompositeFilter000
createDegreeFilter000
createGraphFromNetwork000
createGroup0.0000.0010.000
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromDataFrames0.0000.0010.000
createNetworkFromGraph000
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createSubnetwork000
createView000
createVisualStyle0.0000.0000.001
cybrowserClose000
cybrowserDialog000
cybrowserHide0.0000.0010.000
cybrowserList000
cybrowserSend000
cybrowserShow0.0010.0000.000
cybrowserVersion000
cyrestAPI0.0000.0000.001
cyrestDELETE0.0010.0000.000
cyrestGET000
cyrestPOST000
cyrestPUT000
cytoscapeApiVersions000
cytoscapeFreeMemory0.0010.0000.000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores0.0000.0000.001
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks0.0000.0000.001
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup0.0000.0010.000
deleteNetwork000
deleteSelectedEdges000
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deleteSelfLoops000
deleteStyleMapping0.0000.0000.001
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deleteVisualStyle000
diffusionAdvanced0.0000.0000.001
diffusionBasic000
disableApp000
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doRequestRemote000
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dockPanel0.0010.0000.000
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dot-getRequester000
enableApp000
expandGroup000
exportFilters000
exportImage000
exportNetwork0.0010.0000.000
exportNetworkToNDEx000
exportVisualStyles0.0000.0000.001
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floatPanel000
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getDisabledApps0.0000.0000.001
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getGroupInfo0.0000.0000.001
getInstalledApps0.0010.0000.000
getJupyterBridgeURL000
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getLineStyles000
getNetworkCenter0.0010.0000.000
getNetworkCount000
getNetworkList0.0000.0000.001
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount0.0000.0010.000
getNodeHeight000
getNodePosition0.0000.0000.001
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth000
getNotebookIsRunning0.0000.0010.000
getSandboxReinitialize000
getSelectedEdgeCount0.0000.0000.001
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes0.0000.0000.001
getStyleDependencies000
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getTableColumnNames000
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getTableColumns0.0000.0000.001
getTableValue0.0000.0010.000
getUninstalledApps000
getVisualPropertyDefault0.0000.0000.001
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groupAnnotation0.0000.0000.001
hideAllPanels000
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hideNodes0.0000.0000.001
hidePanel000
hideSelectedEdges000
hideSelectedNodes000
importFilters000
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importNetworkFromNDEx0.0000.0000.001
importVisualStyles000
installApp000
invertEdgeSelection0.0000.0000.001
invertNodeSelection000
layoutCopycat000
layoutNetwork0.0000.0000.001
listGroups000
lockNodeDimensions000
makeSimpleGraph0.0510.0000.052
makeSimpleIgraph0.0400.0120.052
mapTableColumn000
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matchArrowColorToEdge000
mergeNetworks000
notebookExportShowImage0.0000.0000.001
notebookShowImage000
openAppStore000
openSession0.0000.0000.001
paletteColorBrewerAccent0.0020.0020.005
paletteColorBrewerBlues0.0000.0000.001
paletteColorBrewerBrBG0.0010.0000.000
paletteColorBrewerBuGn0.0010.0000.000
paletteColorBrewerBuPu000
paletteColorBrewerDark2000
paletteColorBrewerGnBu0.0000.0000.001
paletteColorBrewerGreens0.0010.0000.001
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paletteColorBrewerOrRd0.0000.0010.000
paletteColorBrewerOranges000
paletteColorBrewerPRGn0.0000.0000.001
paletteColorBrewerPaired0.0000.0000.001
paletteColorBrewerPastel10.0010.0000.001
paletteColorBrewerPastel20.0010.0000.000
paletteColorBrewerPiYG000
paletteColorBrewerPuBu000
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr0.0000.0000.001
paletteColorBrewerPuRd000
paletteColorBrewerPurples0.0000.0010.000
paletteColorBrewerRdBu000
paletteColorBrewerRdPu000
paletteColorBrewerRdYlBu0.0000.0000.001
paletteColorBrewerReds0.0000.0000.001
paletteColorBrewerSet10.0000.0010.000
paletteColorBrewerSet2000
paletteColorBrewerSet3000
paletteColorBrewerYlGn0.0000.0000.001
paletteColorBrewerYlGnBu0.0000.0000.001
paletteColorBrewerYlOrBr0.0010.0000.000
paletteColorBrewerYlOrRd000
paletteColorRandom000
removeNodeCustomGraphics000
renameNetwork0.0000.0000.001
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setEdgePropertyBypass000
setEdgeSelectionColorDefault0.0000.0000.001
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setEdgeSourceArrowColorDefault0.0000.0000.001
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setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass0.0000.0010.000
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setEdgeTargetArrowColorBypass000
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setEdgeTargetArrowColorMapping000
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