Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1679/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.27.0  (landing page)
Alex Pico
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: devel
git_last_commit: 6d1a209
git_last_commit_date: 2024-10-29 10:04:47 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for RCy3 on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: RCy3
Version: 2.27.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RCy3_2.27.0.tar.gz
StartedAt: 2024-12-24 10:16:13 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 10:17:43 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 90.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RCy3_2.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RCy3.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘2.27.0’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RCy3.Rcheck/00check.log’
for details.


Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  0.196   0.035   0.216 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
AddToGroup000
RemoveFromGroup000
UpdateAnnotationBoundedText000
addAnnotationBoundedText000
addAnnotationImage0.0000.0000.001
addAnnotationShape000
addAnnotationText000
addCyEdges0.0010.0000.000
addCyNodes000
analyzeNetwork000
applyFilter000
bundleEdges000
checkNotebookIsRunning000
checkRunningRemote000
clearEdgeBends000
clearEdgePropertyBypass0.0000.0000.001
clearNetworkCenterBypass000
clearNetworkPropertyBypass0.0000.0000.001
clearNetworkZoomBypass000
clearNodeOpacityBypass000
clearNodePropertyBypass000
clearSelection000
cloneNetwork000
closeSession000
collapseGroup0.0010.0000.000
commandEcho000
commandOpenDialog000
commandPause000
commandQuit000
commandRunFile000
commandSleep000
commandsAPI000
commandsGET0.0000.0000.001
commandsHelp000
commandsPOST000
commandsRun000
copyVisualStyle000
createColumnFilter000
createCompositeFilter000
createCytoscapejsFromNetwork000
createDegreeFilter000
createGraphFromNetwork000
createGroup000
createGroupByColumn0.0010.0000.000
createIgraphFromNetwork000
createNetworkFromCytoscapejs000
createNetworkFromDataFrames000
createNetworkFromGraph000
createNetworkFromIgraph000
createSubnetwork000
createView000
createVisualStyle000
cybrowserClose000
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE000
cyrestGET000
cyrestPOST000
cyrestPUT000
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks000
deleteAllVisualStyle000
deleteAnnotation000
deleteDuplicateEdges0.0000.0000.001
deleteGroup000
deleteNetwork0.0000.0000.001
deleteSelectedEdges000
deleteSelectedNodes0.0000.0000.001
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle000
diffusionAdvanced000
diffusionBasic000
disableApp000
doInitializeSandbox000
doRequestRemote000
doSetSandbox000
dockPanel000
dot-exportShowImage000
dot-getDefaultSandbox000
dot-getRequester0.0010.0000.000
enableApp000
expandGroup0.0010.0000.000
exportFilters000
exportImage0.0010.0000.000
exportJPG000
exportNetwork000
exportNetworkToNDEx000
exportPDF000
exportPNG000
exportPS000
exportSVG000
exportVisualStyles000
findRemoteCytoscape000
fitContent0.0010.0000.000
floatPanel000
getAbsSandboxPath000
getAllEdges000
getAllNodes000
getAllStyleMappings000
getAnnotationList0.0000.0000.001
getAppInformation0.0000.0010.000
getAppStatus000
getAppUpdates0.0000.0010.000
getArrowShapes000
getAvailableApps000
getBackgroundColorDefault000
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList000
getCollectionName000
getCollectionNetworks000
getCollectionSuid000
getCurrentSandbox000
getCurrentSandboxName000
getCurrentSandboxPath0.0000.0000.001
getCurrentStyle000
getDefaultSandbox000
getDefaultSandboxPath000
getDisabledApps000
getEdgeColor000
getEdgeCount000
getEdgeInfo0.0000.0010.000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo0.0000.0000.001
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType000
getLayoutPropertyValue0.0000.0010.000
getLineStyles000
getNetworkCenter000
getNetworkCount000
getNetworkList000
getNetworkNDExId000
getNetworkName0.0000.0000.001
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount000
getNodeHeight000
getNodeLabelPosition000
getNodeLabelPositionDefault000
getNodePosition0.0010.0000.000
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth000
getNotebookIsRunning000
getSandboxReinitialize000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes000
getStyleDependencies000
getStyleMapping000
getTableColumnNames000
getTableColumnTypes0.0010.0000.000
getTableColumns000
getTableValue000
getUninstalledApps000
getVisualPropertyDefault000
getVisualPropertyNames000
getVisualStyleJSON000
getVisualStyleNames0.0000.0010.000
groupAnnotation000
hideAllPanels000
hideEdges000
hideNodes0.0010.0000.000
hidePanel000
hideSelectedEdges0.0000.0000.001
hideSelectedNodes000
importFileFromUrl000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx000
importVisualStyles000
installApp000
invertEdgeSelection000
invertNodeSelection0.0010.0000.000
layoutCopycat000
layoutNetwork000
listGroups000
lockNodeDimensions000
makeSimpleGraph0.0860.0000.086
makeSimpleIgraph0.1450.0040.148
mapTableColumn000
mapVisualProperty000
matchArrowColorToEdge000
mergeNetworks000
notebookExportShowImage000
notebookShowImage000
openAppStore0.0010.0000.000
openSession000
paletteColorBrewerAccent0.0020.0030.005
paletteColorBrewerBlues000
paletteColorBrewerBrBG000
paletteColorBrewerBuGn0.0000.0000.001
paletteColorBrewerBuPu000
paletteColorBrewerDark2000
paletteColorBrewerGnBu000
paletteColorBrewerGreens0.0010.0000.000
paletteColorBrewerGreys000
paletteColorBrewerOrRd0.0000.0010.000
paletteColorBrewerOranges000
paletteColorBrewerPRGn0.0000.0000.001
paletteColorBrewerPaired000
paletteColorBrewerPastel1000
paletteColorBrewerPastel20.0000.0000.001
paletteColorBrewerPiYG000
paletteColorBrewerPuBu000
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr0.0010.0000.000
paletteColorBrewerPuRd000
paletteColorBrewerPurples000
paletteColorBrewerRdBu0.0010.0000.000
paletteColorBrewerRdPu000
paletteColorBrewerRdYlBu000
paletteColorBrewerReds0.0010.0000.000
paletteColorBrewerSet10.0000.0000.001
paletteColorBrewerSet2000
paletteColorBrewerSet3000
paletteColorBrewerYlGn0.0000.0000.001
paletteColorBrewerYlGnBu0.0000.0010.000
paletteColorBrewerYlOrBr000
paletteColorBrewerYlOrRd0.0000.0000.001
paletteColorRandom0.0000.0010.000
paletteColorVirdis000
removeNodeCustomGraphics000
renameNetwork000
renameTableColumn000
resetDefaultSandbox000
rotateLayout000
runningRemoteCheck000
sandboxGetFileInfo000
sandboxGetFrom0.0000.0010.000
sandboxInitializer000
sandboxRemove0.0000.0010.000
sandboxRemoveFile000
sandboxSendTo0.0000.0010.000
sandboxSet000
sandboxUrlTo000
saveSession000
scaleLayout000
selectAll000
selectAllEdges000
selectAllNodes000
selectEdges000
selectEdgesAdjacentToNodes000
selectEdgesAdjacentToSelectedNodes000
selectEdgesConnectingSelectedNodes000
selectFirstNeighbors000
selectNodes000
selectNodesConnectedBySelectedEdges000
setBackgroundColorDefault000
setCatchupFilterSecs0.0000.0000.001
setCatchupNetworkSecs000
setCurrentNetwork000
setCurrentSandbox000
setCurrentView000
setDefaultSandbox000
setDefaultSandboxPath000
setEdgeColorBypass000
setEdgeColorDefault000
setEdgeColorMapping000
setEdgeFontFaceBypass000
setEdgeFontFaceDefault000
setEdgeFontFaceMapping000
setEdgeFontSizeBypass000
setEdgeFontSizeDefault000
setEdgeFontSizeMapping000
setEdgeLabelBypass000
setEdgeLabelColorBypass000
setEdgeLabelColorDefault000
setEdgeLabelColorMapping000
setEdgeLabelDefault000
setEdgeLabelMapping000
setEdgeLabelOpacityBypass000
setEdgeLabelOpacityDefault000
setEdgeLabelOpacityMapping000
setEdgeLineStyleBypass000
setEdgeLineStyleDefault000
setEdgeLineStyleMapping000
setEdgeLineWidthBypass000
setEdgeLineWidthDefault000
setEdgeLineWidthMapping000
setEdgeOpacityBypass000
setEdgeOpacityDefault000
setEdgeOpacityMapping000
setEdgePropertyBypass000
setEdgeSelectionColorDefault000
setEdgeSourceArrowColorBypass000
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping0.0000.0000.001
setEdgeSourceArrowShapeBypass000
setEdgeSourceArrowShapeDefault0.0000.0000.001
setEdgeSourceArrowShapeMapping000
setEdgeTargetArrowColorBypass000
setEdgeTargetArrowColorDefault000
setEdgeTargetArrowColorMapping000
setEdgeTargetArrowMapping000
setEdgeTargetArrowShapeBypass000
setEdgeTargetArrowShapeDefault000
setEdgeTargetArrowShapeMapping0.0010.0000.000
setEdgeTooltipBypass000
setEdgeTooltipDefault0.0010.0000.000
setEdgeTooltipMapping000
setLayoutProperties0.0010.0000.000
setModelPropagationSecs000
setNetworkCenterBypass0.0000.0000.001
setNetworkPropertyBypass000
setNetworkZoomBypass0.0000.0000.001
setNodeBorderColorBypass000
setNodeBorderColorDefault000
setNodeBorderColorMapping000
setNodeBorderOpacityBypass000
setNodeBorderOpacityDefault000
setNodeBorderOpacityMapping000
setNodeBorderWidthBypass000
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setNodeBorderWidthMapping000
setNodeColorBypass000
setNodeColorDefault000
setNodeColorMapping0.0010.0000.000
setNodeComboOpacityMapping000
setNodeCustomBarChart0.0010.0000.000
setNodeCustomBoxChart000
setNodeCustomHeatMapChart000
setNodeCustomLineChart000
setNodeCustomLinearGradient000
setNodeCustomPieChart000
setNodeCustomPosition000
setNodeCustomRadialGradient000
setNodeCustomRingChart000
setNodeFillOpacityBypass000
setNodeFillOpacityDefault000
setNodeFillOpacityMapping000
setNodeFontFaceBypass000
setNodeFontFaceDefault000
setNodeFontFaceMapping000
setNodeFontSizeBypass000
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setNodeFontSizeMapping000
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setNodeHeightMapping000
setNodeLabelBypass000
setNodeLabelColorBypass000
setNodeLabelColorDefault000
setNodeLabelColorMapping000
setNodeLabelDefault000
setNodeLabelMapping000
setNodeLabelOpacityBypass000
setNodeLabelOpacityDefault000
setNodeLabelOpacityMapping000
setNodeLabelPositionBypass000
setNodeLabelPositionDefault000
setNodeOpacityBypass000
setNodePositionBypass000
setNodePropertyBypass000
setNodeSelectionColorDefault000
setNodeShapeBypass000
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setNodeSizeBypass000
setNodeSizeDefault000
setNodeSizeMapping000
setNodeTooltipBypass000
setNodeTooltipDefault000
setNodeTooltipMapping000
setNodeWidthBypass000
setNodeWidthDefault000
setNodeWidthMapping000
setNotebookIsRunning000
setSandboxReinitialize000
setStyleDependencies000
setVisualPropertyDefault000
setVisualStyle000
syncNodeCustomGraphicsSize000
toggleGraphicsDetails000
ungroupAnnotation000
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unhideEdges0.0000.0000.001
unhideNodes000
uninstallApp0.0000.0000.001
updateAnnotationImage000
updateAnnotationShape0.0000.0000.001
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updateApp0.0000.0000.001
updateGroupAnnotation000
updateNetworkInNDEx0.0000.0000.001
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updateStyleMapping0.0000.0000.001