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This page was generated on 2024-05-04 11:37:03 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 2024-05-04 02:47:43 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:49:15 -0400 (Sat, 04 May 2024)
EllapsedTime: 93.0 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 beta (2024-04-15 r86425)
* 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 beta (2024-04-15 r86425) -- "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 
  0.163   0.026   0.178 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
AddToGroup000
RemoveFromGroup000
UpdateAnnotationBoundedText000
addAnnotationBoundedText000
addAnnotationImage0.0010.0000.000
addAnnotationShape0.0000.0000.001
addAnnotationText000
addCyEdges000
addCyNodes000
analyzeNetwork000
applyFilter000
bundleEdges000
checkNotebookIsRunning000
checkRunningRemote000
clearEdgeBends0.0000.0000.001
clearEdgePropertyBypass000
clearNetworkCenterBypass000
clearNetworkPropertyBypass000
clearNetworkZoomBypass0.0000.0010.000
clearNodeOpacityBypass000
clearNodePropertyBypass000
clearSelection000
cloneNetwork000
closeSession0.0000.0000.001
collapseGroup000
commandEcho000
commandOpenDialog000
commandPause0.0000.0010.000
commandQuit000
commandRunFile0.0010.0000.000
commandSleep0.0000.0000.001
commandsAPI000
commandsGET000
commandsHelp000
commandsPOST000
commandsRun000
copyVisualStyle000
createColumnFilter000
createCompositeFilter0.0010.0000.000
createCytoscapejsFromNetwork0.0000.0000.001
createDegreeFilter000
createGraphFromNetwork000
createGroup000
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromCytoscapejs000
createNetworkFromDataFrames000
createNetworkFromGraph0.0010.0000.000
createNetworkFromIgraph0.0000.0000.001
createSubnetwork000
createView000
createVisualStyle000
cybrowserClose0.0000.0010.000
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI0.0000.0000.001
cyrestDELETE000
cyrestGET000
cyrestPOST000
cyrestPUT0.0000.0010.000
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks0.0000.0000.001
deleteAllVisualStyle000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup0.0000.0010.000
deleteNetwork000
deleteSelectedEdges000
deleteSelectedNodes000
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle0.0000.0000.001
diffusionAdvanced000
diffusionBasic000
disableApp000
doInitializeSandbox0.0000.0010.000
doRequestRemote000
doSetSandbox0.0010.0000.000
dockPanel000
dot-exportShowImage0.0010.0000.000
dot-getDefaultSandbox0.0000.0000.001
dot-getRequester000
enableApp0.0000.0000.001
expandGroup000
exportFilters000
exportImage000
exportJPG000
exportNetwork000
exportNetworkToNDEx000
exportPDF000
exportPNG000
exportPS0.0000.0000.001
exportSVG000
exportVisualStyles000
findRemoteCytoscape000
fitContent0.0000.0010.000
floatPanel000
getAbsSandboxPath000
getAllEdges000
getAllNodes000
getAllStyleMappings0.0000.0000.001
getAnnotationList000
getAppInformation000
getAppStatus000
getAppUpdates0.0000.0010.000
getArrowShapes000
getAvailableApps000
getBackgroundColorDefault000
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList000
getCollectionName0.0000.0000.001
getCollectionNetworks000
getCollectionSuid000
getCurrentSandbox000
getCurrentSandboxName000
getCurrentSandboxPath000
getCurrentStyle000
getDefaultSandbox000
getDefaultSandboxPath000
getDisabledApps0.0000.0000.001
getEdgeColor000
getEdgeCount000
getEdgeInfo0.0010.0010.000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList0.0000.0000.001
getFirstNeighbors0.0010.0000.000
getGroupInfo000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType000
getLayoutPropertyValue0.0000.0000.001
getLineStyles000
getNetworkCenter000
getNetworkCount000
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid0.0000.0010.001
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount000
getNodeHeight000
getNodeLabelPosition000
getNodeLabelPositionDefault0.0000.0000.001
getNodePosition000
getNodeProperty0.0000.0010.000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth000
getNotebookIsRunning000
getSandboxReinitialize000
getSelectedEdgeCount0.0000.0000.001
getSelectedEdges000
getSelectedNodeCount0.0000.0010.000
getSelectedNodes000
getStyleDependencies000
getStyleMapping000
getTableColumnNames000
getTableColumnTypes0.0000.0000.001
getTableColumns000
getTableValue000
getUninstalledApps000
getVisualPropertyDefault0.0000.0010.000
getVisualPropertyNames000
getVisualStyleJSON000
getVisualStyleNames000
groupAnnotation000
hideAllPanels000
hideEdges0.0010.0000.000
hideNodes0.0000.0000.001
hidePanel0.0010.0000.000
hideSelectedEdges000
hideSelectedNodes000
importFileFromUrl000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx0.0000.0000.001
importVisualStyles0.0010.0000.000
installApp000
invertEdgeSelection000
invertNodeSelection000
layoutCopycat000
layoutNetwork000
listGroups000
lockNodeDimensions000
makeSimpleGraph0.0550.0010.055
makeSimpleIgraph0.0600.0040.064
mapTableColumn0.0000.0000.001
mapVisualProperty000
matchArrowColorToEdge000
mergeNetworks000
notebookExportShowImage000
notebookShowImage000
openAppStore000
openSession000
paletteColorBrewerAccent0.0020.0030.005
paletteColorBrewerBlues0.0010.0010.000
paletteColorBrewerBrBG0.0000.0000.001
paletteColorBrewerBuGn0.0000.0000.001
paletteColorBrewerBuPu000
paletteColorBrewerDark20.0010.0000.000
paletteColorBrewerGnBu000
paletteColorBrewerGreens0.0000.0000.001
paletteColorBrewerGreys000
paletteColorBrewerOrRd000
paletteColorBrewerOranges000
paletteColorBrewerPRGn0.0000.0010.001
paletteColorBrewerPaired0.0000.0000.001
paletteColorBrewerPastel1000
paletteColorBrewerPastel20.0010.0000.000
paletteColorBrewerPiYG000
paletteColorBrewerPuBu0.0000.0000.001
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr0.0010.0000.000
paletteColorBrewerPuRd000
paletteColorBrewerPurples0.0000.0000.001
paletteColorBrewerRdBu000
paletteColorBrewerRdPu0.0010.0000.000
paletteColorBrewerRdYlBu0.0010.0000.000
paletteColorBrewerReds0.0000.0000.001
paletteColorBrewerSet10.0000.0000.001
paletteColorBrewerSet2000
paletteColorBrewerSet30.0010.0000.000
paletteColorBrewerYlGn000
paletteColorBrewerYlGnBu0.0000.0000.001
paletteColorBrewerYlOrBr000
paletteColorBrewerYlOrRd0.0010.0000.000
paletteColorRandom0.0010.0000.000
paletteColorVirdis000
removeNodeCustomGraphics000
renameNetwork000
renameTableColumn0.0000.0000.001
resetDefaultSandbox000
rotateLayout0.0000.0010.000
runningRemoteCheck000
sandboxGetFileInfo000
sandboxGetFrom000
sandboxInitializer000
sandboxRemove0.0000.0000.001
sandboxRemoveFile000
sandboxSendTo0.0000.0010.000
sandboxSet000
sandboxUrlTo0.0000.0010.000
saveSession000
scaleLayout000
selectAll000
selectAllEdges000
selectAllNodes0.0000.0000.001
selectEdges000
selectEdgesAdjacentToNodes0.0000.0010.000
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selectFirstNeighbors0.0000.0000.001
selectNodes000
selectNodesConnectedBySelectedEdges0.0000.0010.000
setBackgroundColorDefault000
setCatchupFilterSecs000
setCatchupNetworkSecs0.0000.0010.000
setCurrentNetwork0.0000.0000.001
setCurrentSandbox0.0010.0000.000
setCurrentView000
setDefaultSandbox000
setDefaultSandboxPath000
setEdgeColorBypass000
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setEdgeColorMapping0.0000.0000.001
setEdgeFontFaceBypass000
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setEdgeLabelColorMapping000
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setEdgeLabelMapping000
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setEdgeLineStyleBypass000
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setEdgeLineStyleMapping000
setEdgeLineWidthBypass0.0000.0000.001
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setEdgeLineWidthMapping000
setEdgeOpacityBypass000
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setEdgeOpacityMapping0.0000.0000.001
setEdgePropertyBypass0.0010.0000.000
setEdgeSelectionColorDefault000
setEdgeSourceArrowColorBypass000
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass0.0000.0010.001
setEdgeSourceArrowShapeDefault000
setEdgeSourceArrowShapeMapping000
setEdgeTargetArrowColorBypass000
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setEdgeTargetArrowColorMapping0.0000.0000.001
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setEdgeTooltipBypass000
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