Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1691/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.26.0  (landing page)
Alex Pico
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: RELEASE_3_20
git_last_commit: c3be18a
git_last_commit_date: 2024-10-29 10:04:47 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for RCy3 on kjohnson1

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: 2.26.0
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_2.26.0.tar.gz
StartedAt: 2024-12-21 06:10:39 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 06:12:07 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 87.9 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_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RCy3.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘2.26.0’
* package encoding: UTF-8
* 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-3.20-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-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 
  0.224   0.058   0.275 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
AddToGroup0.0000.0000.001
RemoveFromGroup0.0000.0000.001
UpdateAnnotationBoundedText000
addAnnotationBoundedText000
addAnnotationImage000
addAnnotationShape000
addAnnotationText0.0000.0000.001
addCyEdges000
addCyNodes000
analyzeNetwork0.0010.0000.000
applyFilter0.0000.0000.001
bundleEdges000
checkNotebookIsRunning000
checkRunningRemote0.0000.0000.001
clearEdgeBends000
clearEdgePropertyBypass000
clearNetworkCenterBypass000
clearNetworkPropertyBypass000
clearNetworkZoomBypass000
clearNodeOpacityBypass000
clearNodePropertyBypass000
clearSelection000
cloneNetwork000
closeSession0.0010.0000.001
collapseGroup000
commandEcho000
commandOpenDialog000
commandPause000
commandQuit000
commandRunFile000
commandSleep0.0010.0000.001
commandsAPI000
commandsGET0.0000.0010.000
commandsHelp000
commandsPOST0.0000.0000.001
commandsRun000
copyVisualStyle000
createColumnFilter000
createCompositeFilter000
createCytoscapejsFromNetwork0.0000.0000.001
createDegreeFilter000
createGraphFromNetwork0.0010.0000.000
createGroup000
createGroupByColumn0.0000.0000.001
createIgraphFromNetwork000
createNetworkFromCytoscapejs000
createNetworkFromDataFrames000
createNetworkFromGraph0.0000.0000.001
createNetworkFromIgraph000
createSubnetwork000
createView0.0010.0000.000
createVisualStyle000
cybrowserClose0.0000.0000.001
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow0.0000.0010.000
cybrowserVersion000
cyrestAPI0.0000.0000.001
cyrestDELETE000
cyrestGET000
cyrestPOST000
cyrestPUT0.0000.0000.001
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus0.0000.0000.001
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo0.0000.0000.001
deleteAllNetworks000
deleteAllVisualStyle000
deleteAnnotation0.0000.0000.001
deleteDuplicateEdges000
deleteGroup0.0010.0000.000
deleteNetwork000
deleteSelectedEdges000
deleteSelectedNodes000
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle000
diffusionAdvanced000
diffusionBasic000
disableApp000
doInitializeSandbox0.0000.0010.000
doRequestRemote0.0000.0000.001
doSetSandbox000
dockPanel000
dot-exportShowImage000
dot-getDefaultSandbox000
dot-getRequester000
enableApp000
expandGroup000
exportFilters0.0010.0000.000
exportImage000
exportJPG000
exportNetwork000
exportNetworkToNDEx0.0000.0000.001
exportPDF000
exportPNG0.0000.0010.000
exportPS000
exportSVG0.0000.0000.001
exportVisualStyles000
findRemoteCytoscape0.0010.0000.000
fitContent000
floatPanel000
getAbsSandboxPath000
getAllEdges000
getAllNodes0.0000.0000.001
getAllStyleMappings000
getAnnotationList000
getAppInformation000
getAppStatus000
getAppUpdates000
getArrowShapes000
getAvailableApps000
getBackgroundColorDefault000
getBrowserClientChannel0.0010.0000.000
getBrowserClientJs0.0000.0000.001
getCollectionList000
getCollectionName000
getCollectionNetworks0.0000.0000.001
getCollectionSuid000
getCurrentSandbox000
getCurrentSandboxName0.0000.0000.001
getCurrentSandboxPath000
getCurrentStyle000
getDefaultSandbox000
getDefaultSandboxPath000
getDisabledApps000
getEdgeColor000
getEdgeCount000
getEdgeInfo000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo0.0010.0000.000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType0.0000.0000.001
getLayoutPropertyValue000
getLineStyles000
getNetworkCenter0.0000.0000.001
getNetworkCount000
getNetworkList0.0000.0010.000
getNetworkNDExId000
getNetworkName000
getNetworkProperty0.0000.0010.000
getNetworkSuid000
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount0.0000.0010.000
getNodeHeight000
getNodeLabelPosition0.0000.0000.001
getNodeLabelPositionDefault0.0010.0010.000
getNodePosition000
getNodeProperty0.0000.0000.001
getNodeSelectionColorDefault0.0000.0010.000
getNodeShapes000
getNodeSize0.0000.0000.001
getNodeWidth0.0000.0010.000
getNotebookIsRunning000
getSandboxReinitialize000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount0.0000.0010.000
getSelectedNodes000
getStyleDependencies000
getStyleMapping000
getTableColumnNames000
getTableColumnTypes000
getTableColumns000
getTableValue000
getUninstalledApps000
getVisualPropertyDefault000
getVisualPropertyNames0.0000.0000.001
getVisualStyleJSON000
getVisualStyleNames0.0000.0010.000
groupAnnotation000
hideAllPanels000
hideEdges000
hideNodes000
hidePanel0.0000.0010.000
hideSelectedEdges0.0000.0000.001
hideSelectedNodes000
importFileFromUrl000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx000
importVisualStyles0.0010.0000.000
installApp000
invertEdgeSelection000
invertNodeSelection000
layoutCopycat000
layoutNetwork0.0000.0010.000
listGroups000
lockNodeDimensions0.0000.0000.001
makeSimpleGraph0.0610.0000.064
makeSimpleIgraph0.1400.0070.148
mapTableColumn000
mapVisualProperty000
matchArrowColorToEdge000
mergeNetworks0.0000.0010.000
notebookExportShowImage000
notebookShowImage000
openAppStore0.0010.0010.000
openSession000
paletteColorBrewerAccent0.0050.0010.005
paletteColorBrewerBlues000
paletteColorBrewerBrBG000
paletteColorBrewerBuGn000
paletteColorBrewerBuPu0.0000.0000.001
paletteColorBrewerDark20.0010.0010.000
paletteColorBrewerGnBu000
paletteColorBrewerGreens000
paletteColorBrewerGreys0.0000.0010.000
paletteColorBrewerOrRd000
paletteColorBrewerOranges0.0000.0010.001
paletteColorBrewerPRGn000
paletteColorBrewerPaired0.0010.0000.000
paletteColorBrewerPastel1000
paletteColorBrewerPastel2000
paletteColorBrewerPiYG0.0000.0000.001
paletteColorBrewerPuBu000
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr000
paletteColorBrewerPuRd0.0010.0000.000
paletteColorBrewerPurples000
paletteColorBrewerRdBu0.0000.0000.001
paletteColorBrewerRdPu000
paletteColorBrewerRdYlBu0.0000.0010.000
paletteColorBrewerReds000
paletteColorBrewerSet1000
paletteColorBrewerSet20.0010.0000.000
paletteColorBrewerSet30.0000.0000.001
paletteColorBrewerYlGn0.0000.0010.000
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr000
paletteColorBrewerYlOrRd000
paletteColorRandom0.0010.0000.002
paletteColorVirdis000
removeNodeCustomGraphics0.0010.0000.000
renameNetwork0.0000.0000.001
renameTableColumn000
resetDefaultSandbox000
rotateLayout0.0000.0000.001
runningRemoteCheck000
sandboxGetFileInfo000
sandboxGetFrom000
sandboxInitializer000
sandboxRemove000
sandboxRemoveFile0.0000.0010.000
sandboxSendTo0.0000.0000.001
sandboxSet000
sandboxUrlTo000
saveSession0.0000.0000.001
scaleLayout000
selectAll000
selectAllEdges000
selectAllNodes0.0000.0000.001
selectEdges000
selectEdgesAdjacentToNodes0.0010.0000.000
selectEdgesAdjacentToSelectedNodes0.0000.0000.001
selectEdgesConnectingSelectedNodes000
selectFirstNeighbors0.0010.0000.000
selectNodes000
selectNodesConnectedBySelectedEdges000
setBackgroundColorDefault000
setCatchupFilterSecs0.0000.0010.000
setCatchupNetworkSecs0.0010.0000.000
setCurrentNetwork0.0000.0000.001
setCurrentSandbox000
setCurrentView000
setDefaultSandbox000
setDefaultSandboxPath000
setEdgeColorBypass000
setEdgeColorDefault0.0000.0010.000
setEdgeColorMapping000
setEdgeFontFaceBypass000
setEdgeFontFaceDefault000
setEdgeFontFaceMapping000
setEdgeFontSizeBypass000
setEdgeFontSizeDefault000
setEdgeFontSizeMapping000
setEdgeLabelBypass000
setEdgeLabelColorBypass000
setEdgeLabelColorDefault0.0010.0010.000
setEdgeLabelColorMapping000
setEdgeLabelDefault000
setEdgeLabelMapping0.0010.0000.000
setEdgeLabelOpacityBypass000
setEdgeLabelOpacityDefault000
setEdgeLabelOpacityMapping000
setEdgeLineStyleBypass0.0000.0000.001
setEdgeLineStyleDefault000
setEdgeLineStyleMapping000
setEdgeLineWidthBypass000
setEdgeLineWidthDefault000
setEdgeLineWidthMapping0.0000.0000.001
setEdgeOpacityBypass000
setEdgeOpacityDefault000
setEdgeOpacityMapping000
setEdgePropertyBypass000
setEdgeSelectionColorDefault0.0000.0010.000
setEdgeSourceArrowColorBypass000
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass000
setEdgeSourceArrowShapeDefault000
setEdgeSourceArrowShapeMapping000
setEdgeTargetArrowColorBypass0.0000.0000.001
setEdgeTargetArrowColorDefault000
setEdgeTargetArrowColorMapping000
setEdgeTargetArrowMapping000
setEdgeTargetArrowShapeBypass000
setEdgeTargetArrowShapeDefault000
setEdgeTargetArrowShapeMapping0.0000.0010.000
setEdgeTooltipBypass0.0000.0000.001
setEdgeTooltipDefault000
setEdgeTooltipMapping0.0010.0000.000
setLayoutProperties000
setModelPropagationSecs0.0000.0000.001
setNetworkCenterBypass000
setNetworkPropertyBypass000
setNetworkZoomBypass000
setNodeBorderColorBypass000
setNodeBorderColorDefault000
setNodeBorderColorMapping000
setNodeBorderOpacityBypass000
setNodeBorderOpacityDefault000
setNodeBorderOpacityMapping0.0000.0000.001
setNodeBorderWidthBypass000
setNodeBorderWidthDefault0.0010.0000.000
setNodeBorderWidthMapping000
setNodeColorBypass000
setNodeColorDefault000
setNodeColorMapping000
setNodeComboOpacityMapping000
setNodeCustomBarChart000
setNodeCustomBoxChart000
setNodeCustomHeatMapChart000
setNodeCustomLineChart000
setNodeCustomLinearGradient0.0000.0000.001
setNodeCustomPieChart000
setNodeCustomPosition000
setNodeCustomRadialGradient000
setNodeCustomRingChart000
setNodeFillOpacityBypass000
setNodeFillOpacityDefault000
setNodeFillOpacityMapping000
setNodeFontFaceBypass000
setNodeFontFaceDefault000
setNodeFontFaceMapping000
setNodeFontSizeBypass0.0000.0000.001
setNodeFontSizeDefault0.0000.0010.000
setNodeFontSizeMapping000
setNodeHeightBypass000
setNodeHeightDefault0.0000.0000.001
setNodeHeightMapping000
setNodeLabelBypass000
setNodeLabelColorBypass0.0000.0000.001
setNodeLabelColorDefault000
setNodeLabelColorMapping0.0010.0000.000
setNodeLabelDefault000
setNodeLabelMapping000
setNodeLabelOpacityBypass0.0010.0000.000
setNodeLabelOpacityDefault000
setNodeLabelOpacityMapping0.0000.0000.001
setNodeLabelPositionBypass000
setNodeLabelPositionDefault000
setNodeOpacityBypass000
setNodePositionBypass0.0000.0000.001
setNodePropertyBypass000
setNodeSelectionColorDefault0.0000.0010.000
setNodeShapeBypass0.0000.0000.001
setNodeShapeDefault000
setNodeShapeMapping0.0000.0010.000
setNodeSizeBypass000
setNodeSizeDefault000
setNodeSizeMapping000
setNodeTooltipBypass000
setNodeTooltipDefault000
setNodeTooltipMapping000
setNodeWidthBypass000
setNodeWidthDefault000
setNodeWidthMapping0.0010.0000.001
setNotebookIsRunning0.0000.0000.003
setSandboxReinitialize0.0010.0000.000
setStyleDependencies000
setVisualPropertyDefault000
setVisualStyle0.0000.0000.001
syncNodeCustomGraphicsSize000
toggleGraphicsDetails0.0010.0000.004
ungroupAnnotation000
unhideAll000
unhideEdges000
unhideNodes000
uninstallApp000
updateAnnotationImage000
updateAnnotationShape000
updateAnnotationText000
updateApp0.0000.0000.001
updateGroupAnnotation000
updateNetworkInNDEx000
updateStyleDefaults000
updateStyleMapping0.0010.0000.000