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This page was generated on 2024-05-04 11:39:49 -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 lconway


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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCy3_2.24.0.tar.gz
StartedAt: 2024-05-04 00:18:46 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:20:25 -0400 (Sat, 04 May 2024)
EllapsedTime: 98.9 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCy3_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RCy3.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘2.24.0’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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


Installation output

RCy3.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  0.193   0.078   0.274 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
AddToGroup000
RemoveFromGroup000
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addAnnotationBoundedText000
addAnnotationImage0.0000.0010.000
addAnnotationShape000
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analyzeNetwork0.0000.0010.000
applyFilter000
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checkNotebookIsRunning000
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clearNetworkPropertyBypass0.0000.0010.000
clearNetworkZoomBypass000
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clearNodePropertyBypass000
clearSelection000
cloneNetwork000
closeSession0.0000.0000.001
collapseGroup000
commandEcho000
commandOpenDialog000
commandPause0.0000.0000.001
commandQuit0.0000.0000.001
commandRunFile000
commandSleep0.0010.0010.000
commandsAPI000
commandsGET000
commandsHelp000
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commandsRun000
copyVisualStyle000
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createDegreeFilter000
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createGroup0.0000.0000.001
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromCytoscapejs000
createNetworkFromDataFrames000
createNetworkFromGraph0.0000.0010.001
createNetworkFromIgraph0.0000.0000.001
createSubnetwork0.0000.0000.001
createView000
createVisualStyle0.0000.0000.001
cybrowserClose000
cybrowserDialog000
cybrowserHide000
cybrowserList0.0010.0000.000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE000
cyrestGET000
cyrestPOST000
cyrestPUT000
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores0.0000.0010.001
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks000
deleteAllVisualStyle000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup0.0000.0000.001
deleteNetwork0.0010.0000.000
deleteSelectedEdges000
deleteSelectedNodes000
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn0.0000.0000.001
deleteVisualStyle0.0000.0010.000
diffusionAdvanced000
diffusionBasic000
disableApp000
doInitializeSandbox000
doRequestRemote0.0000.0010.000
doSetSandbox000
dockPanel000
dot-exportShowImage000
dot-getDefaultSandbox0.0000.0000.001
dot-getRequester0.0000.0000.001
enableApp000
expandGroup0.0010.0000.000
exportFilters0.0000.0010.000
exportImage000
exportJPG000
exportNetwork000
exportNetworkToNDEx000
exportPDF000
exportPNG000
exportPS000
exportSVG000
exportVisualStyles0.0010.0010.000
findRemoteCytoscape000
fitContent000
floatPanel000
getAbsSandboxPath000
getAllEdges000
getAllNodes000
getAllStyleMappings000
getAnnotationList0.0000.0010.000
getAppInformation000
getAppStatus000
getAppUpdates000
getArrowShapes000
getAvailableApps000
getBackgroundColorDefault000
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList000
getCollectionName000
getCollectionNetworks000
getCollectionSuid0.0010.0010.000
getCurrentSandbox0.0000.0000.001
getCurrentSandboxName0.0000.0010.001
getCurrentSandboxPath000
getCurrentStyle000
getDefaultSandbox000
getDefaultSandboxPath000
getDisabledApps000
getEdgeColor000
getEdgeCount0.0010.0000.000
getEdgeInfo0.0000.0010.000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape0.0000.0000.001
getFilterList000
getFirstNeighbors000
getGroupInfo000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames0.0000.0000.001
getLayoutPropertyNames0.0010.0000.000
getLayoutPropertyType000
getLayoutPropertyValue000
getLineStyles0.0000.0000.001
getNetworkCenter000
getNetworkCount0.0000.0000.001
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty0.0000.0000.001
getNetworkSuid000
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom0.0010.0000.000
getNodeColor000
getNodeCount0.0000.0000.001
getNodeHeight000
getNodeLabelPosition0.0010.0000.000
getNodeLabelPositionDefault0.0000.0010.000
getNodePosition000
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize0.0000.0010.000
getNodeWidth0.0000.0000.001
getNotebookIsRunning000
getSandboxReinitialize000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes000
getStyleDependencies0.0010.0000.000
getStyleMapping000
getTableColumnNames000
getTableColumnTypes000
getTableColumns000
getTableValue000
getUninstalledApps000
getVisualPropertyDefault0.0000.0000.001
getVisualPropertyNames000
getVisualStyleJSON000
getVisualStyleNames0.0010.0000.000
groupAnnotation0.0000.0000.001
hideAllPanels000
hideEdges000
hideNodes000
hidePanel000
hideSelectedEdges0.0000.0010.001
hideSelectedNodes0.0010.0000.000
importFileFromUrl000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx0.0000.0010.000
importVisualStyles0.0000.0000.001
installApp000
invertEdgeSelection000
invertNodeSelection000
layoutCopycat0.0000.0010.000
layoutNetwork0.0000.0000.001
listGroups000
lockNodeDimensions0.0010.0010.000
makeSimpleGraph0.0800.0010.081
makeSimpleIgraph0.0970.0100.109
mapTableColumn000
mapVisualProperty0.0000.0010.000
matchArrowColorToEdge000
mergeNetworks0.0000.0010.000
notebookExportShowImage000
notebookShowImage0.0010.0000.000
openAppStore000
openSession0.0000.0010.000
paletteColorBrewerAccent0.0050.0010.006
paletteColorBrewerBlues000
paletteColorBrewerBrBG000
paletteColorBrewerBuGn0.0010.0000.001
paletteColorBrewerBuPu000
paletteColorBrewerDark2000
paletteColorBrewerGnBu0.0000.0000.001
paletteColorBrewerGreens0.0000.0010.000
paletteColorBrewerGreys000
paletteColorBrewerOrRd000
paletteColorBrewerOranges0.0000.0000.001
paletteColorBrewerPRGn000
paletteColorBrewerPaired0.0010.0010.000
paletteColorBrewerPastel1000
paletteColorBrewerPastel20.0000.0000.001
paletteColorBrewerPiYG0.0000.0000.001
paletteColorBrewerPuBu000
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr000
paletteColorBrewerPuRd0.0000.0010.001
paletteColorBrewerPurples000
paletteColorBrewerRdBu000
paletteColorBrewerRdPu000
paletteColorBrewerRdYlBu0.0000.0000.001
paletteColorBrewerReds0.0010.0010.000
paletteColorBrewerSet1000
paletteColorBrewerSet20.0000.0010.000
paletteColorBrewerSet3000
paletteColorBrewerYlGn0.0000.0010.001
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr0.0000.0010.000
paletteColorBrewerYlOrRd000
paletteColorRandom0.0000.0010.000
paletteColorVirdis0.0000.0000.001
removeNodeCustomGraphics0.0000.0010.000
renameNetwork000
renameTableColumn0.0010.0000.000
resetDefaultSandbox000
rotateLayout0.0010.0000.000
runningRemoteCheck000
sandboxGetFileInfo000
sandboxGetFrom0.0000.0000.001
sandboxInitializer0.0000.0000.001
sandboxRemove000
sandboxRemoveFile0.0000.0010.000
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sandboxUrlTo000
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selectAllNodes000
selectEdges000
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selectEdgesConnectingSelectedNodes0.0000.0010.001
selectFirstNeighbors0.0000.0000.001
selectNodes0.0010.0010.001
selectNodesConnectedBySelectedEdges000
setBackgroundColorDefault000
setCatchupFilterSecs000
setCatchupNetworkSecs0.0000.0010.000
setCurrentNetwork000
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