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This page was generated on 2024-05-31 17:03:11 -0400 (Fri, 31 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 1706/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.24.0  (landing page)
Alex Pico
Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: RELEASE_3_19
git_last_commit: ca074c6
git_last_commit_date: 2024-04-30 10:46:27 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for RCy3 on nebbiolo1


To the developers/maintainers of the RCy3 package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RCy3
Version: 2.24.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RCy3_2.24.0.tar.gz
StartedAt: 2024-05-31 07:15:18 -0400 (Fri, 31 May 2024)
EndedAt: 2024-05-31 07:16:59 -0400 (Fri, 31 May 2024)
EllapsedTime: 101.4 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RCy3_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RCy3.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘2.24.0’
* 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... 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
.checkHexColor: no visible global function definition for ‘colors’
.edgeNameToEdgeSUID: no visible binding for global variable ‘SUID’
.nodeNameToNodeSUID: no visible binding for global variable ‘SUID’
createNetworkFromDataFrames: no visible binding for global variable
  ‘SUID’
Undefined global functions or variables:
  SUID colors
Consider adding
  importFrom("grDevices", "colors")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) importFileFromUrl.Rd:24: Lost braces; missing escapes or markup?
    24 | dict: {'filePath': <new file's absolute path in Cytoscape workstation>, 'fileByteCount': number of bytes read}
       |       ^
checkRd: (-1) sandboxGetFileInfo.Rd:17: Lost braces; missing escapes or markup?
    17 | dict: {'filePath': <full path on Cytoscape workstation>, 'modifiedTime': <last changed time, '' if file doesn't exist>, 'isFile': <True if file, False if directory>}
       |       ^
checkRd: (-1) sandboxRemove.Rd:15: Lost braces; missing escapes or markup?
    15 | dict: {'sandboxPath': <directory on Cytoscape workstation>, 'existed': <True if sandbox existed>}
       |       ^
checkRd: (-1) sandboxRemoveFile.Rd:17: Lost braces; missing escapes or markup?
    17 | dict: {'filePath': <file's absolute path in Cytoscape workstation>, 'existed': True if file existed before being deleted}
       |       ^
checkRd: (-1) sandboxUrlTo.Rd:27: Lost braces; missing escapes or markup?
    27 | dict: {'filePath': <new file's absolute path in Cytoscape workstation>, 'fileByteCount': number of bytes read}
       |       ^
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/RCy3.Rcheck/00check.log’
for details.


Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.185   0.032   0.205 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
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RemoveFromGroup000
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addAnnotationBoundedText000
addAnnotationImage000
addAnnotationShape0.0010.0000.000
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addCyNodes000
analyzeNetwork000
applyFilter000
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checkNotebookIsRunning0.0010.0000.000
checkRunningRemote000
clearEdgeBends0.0000.0000.001
clearEdgePropertyBypass000
clearNetworkCenterBypass000
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clearNetworkZoomBypass000
clearNodeOpacityBypass0.0010.0000.000
clearNodePropertyBypass000
clearSelection0.0000.0000.001
cloneNetwork000
closeSession000
collapseGroup000
commandEcho000
commandOpenDialog0.0010.0000.000
commandPause000
commandQuit0.0000.0000.001
commandRunFile000
commandSleep000
commandsAPI0.0000.0010.000
commandsGET000
commandsHelp000
commandsPOST000
commandsRun000
copyVisualStyle000
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createCompositeFilter000
createCytoscapejsFromNetwork000
createDegreeFilter000
createGraphFromNetwork000
createGroup0.0010.0000.000
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromCytoscapejs000
createNetworkFromDataFrames000
createNetworkFromGraph000
createNetworkFromIgraph000
createSubnetwork0.0000.0000.001
createView0.0000.0010.000
createVisualStyle000
cybrowserClose000
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend0.0000.0000.001
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE000
cyrestGET0.0010.0000.000
cyrestPOST000
cyrestPUT0.0000.0000.001
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks000
deleteAllVisualStyle000
deleteAnnotation0.0000.0000.001
deleteDuplicateEdges000
deleteGroup000
deleteNetwork0.0000.0010.000
deleteSelectedEdges000
deleteSelectedNodes000
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle0.0000.0000.001
diffusionAdvanced000
diffusionBasic000
disableApp000
doInitializeSandbox000
doRequestRemote000
doSetSandbox000
dockPanel0.0010.0000.000
dot-exportShowImage000
dot-getDefaultSandbox000
dot-getRequester000
enableApp0.0000.0000.001
expandGroup000
exportFilters000
exportImage000
exportJPG000
exportNetwork0.0010.0000.000
exportNetworkToNDEx000
exportPDF000
exportPNG000
exportPS000
exportSVG000
exportVisualStyles000
findRemoteCytoscape0.0000.0000.001
fitContent000
floatPanel000
getAbsSandboxPath0.0010.0000.000
getAllEdges000
getAllNodes0.0000.0000.001
getAllStyleMappings000
getAnnotationList000
getAppInformation000
getAppStatus000
getAppUpdates0.0000.0000.001
getArrowShapes0.0000.0010.000
getAvailableApps000
getBackgroundColorDefault000
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList0.0000.0010.000
getCollectionName000
getCollectionNetworks000
getCollectionSuid000
getCurrentSandbox0.0000.0000.001
getCurrentSandboxName0.0000.0010.000
getCurrentSandboxPath000
getCurrentStyle0.0010.0000.000
getDefaultSandbox000
getDefaultSandboxPath000
getDisabledApps000
getEdgeColor000
getEdgeCount000
getEdgeInfo000
getEdgeLineStyle000
getEdgeLineWidth0.0010.0000.001
getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors0.0000.0000.001
getGroupInfo000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType0.0000.0000.001
getLayoutPropertyValue000
getLineStyles000
getNetworkCenter000
getNetworkCount000
getNetworkList0.0010.0000.000
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom000
getNodeColor0.0000.0010.000
getNodeCount000
getNodeHeight000
getNodeLabelPosition000
getNodeLabelPositionDefault000
getNodePosition0.0000.0010.000
getNodeProperty0.0000.0000.001
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth000
getNotebookIsRunning0.0000.0000.001
getSandboxReinitialize000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes000
getStyleDependencies0.0000.0010.000
getStyleMapping000
getTableColumnNames000
getTableColumnTypes000
getTableColumns000
getTableValue0.0010.0000.000
getUninstalledApps000
getVisualPropertyDefault000
getVisualPropertyNames000
getVisualStyleJSON000
getVisualStyleNames000
groupAnnotation000
hideAllPanels0.0010.0000.001
hideEdges000
hideNodes000
hidePanel000
hideSelectedEdges000
hideSelectedNodes000
importFileFromUrl000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx0.0000.0010.000
importVisualStyles000
installApp000
invertEdgeSelection000
invertNodeSelection0.0000.0000.001
layoutCopycat000
layoutNetwork000
listGroups0.0000.0000.001
lockNodeDimensions0.0000.0010.000
makeSimpleGraph0.0580.0160.074
makeSimpleIgraph0.0680.0000.068
mapTableColumn0.0010.0000.001
mapVisualProperty000
matchArrowColorToEdge0.0090.0000.009
mergeNetworks000
notebookExportShowImage000
notebookShowImage0.0010.0000.000
openAppStore000
openSession000
paletteColorBrewerAccent0.0010.0030.004
paletteColorBrewerBlues0.0010.0000.000
paletteColorBrewerBrBG0.0010.0010.000
paletteColorBrewerBuGn000
paletteColorBrewerBuPu000
paletteColorBrewerDark20.0000.0000.001
paletteColorBrewerGnBu0.0010.0000.001
paletteColorBrewerGreens000
paletteColorBrewerGreys000
paletteColorBrewerOrRd000
paletteColorBrewerOranges0.0000.0000.001
paletteColorBrewerPRGn0.0010.0000.001
paletteColorBrewerPaired000
paletteColorBrewerPastel1000
paletteColorBrewerPastel2000
paletteColorBrewerPiYG0.0010.0000.001
paletteColorBrewerPuBu0.0010.0000.000
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr000
paletteColorBrewerPuRd000
paletteColorBrewerPurples0.0010.0000.001
paletteColorBrewerRdBu000
paletteColorBrewerRdPu000
paletteColorBrewerRdYlBu000
paletteColorBrewerReds000
paletteColorBrewerSet1000
paletteColorBrewerSet20.0010.0000.001
paletteColorBrewerSet3000
paletteColorBrewerYlGn000
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr000
paletteColorBrewerYlOrRd0.0000.0000.001
paletteColorRandom0.0000.0000.001
paletteColorVirdis0.0000.0000.001
removeNodeCustomGraphics000
renameNetwork000
renameTableColumn0.0010.0000.001
resetDefaultSandbox000
rotateLayout000
runningRemoteCheck000
sandboxGetFileInfo000
sandboxGetFrom0.0000.0000.001
sandboxInitializer0.0000.0010.000
sandboxRemove000
sandboxRemoveFile000
sandboxSendTo000
sandboxSet0.0000.0000.001
sandboxUrlTo000
saveSession000
scaleLayout000
selectAll000
selectAllEdges0.0000.0000.001
selectAllNodes000
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selectEdgesAdjacentToSelectedNodes000
selectEdgesConnectingSelectedNodes000
selectFirstNeighbors000
selectNodes000
selectNodesConnectedBySelectedEdges0.0000.0000.001
setBackgroundColorDefault0.0000.0010.000
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setCurrentNetwork000
setCurrentSandbox000
setCurrentView000
setDefaultSandbox0.0010.0000.000
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setEdgeLabelOpacityBypass0.0010.0000.001
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setEdgePropertyBypass000
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