Alex Pico
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/RCy3 |
| git_branch: RELEASE_3_13 |
| git_last_commit: 5bb5011 |
| git_last_commit_date: 2021-08-09 14:24:15 -0400 (Mon, 09 Aug 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:18 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the RCy3 package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1526/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RCy3 2.12.4 (landing page) Alex Pico
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: RCy3 |
| Version: 2.12.4 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCy3.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RCy3_2.12.4.tar.gz |
| StartedAt: 2021-10-15 04:11:50 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:16:17 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 266.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RCy3.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCy3.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RCy3_2.12.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/RCy3.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RCy3/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCy3' version '2.12.4'
* 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 whether package 'RCy3' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.edgeNameToEdgeSUID: no visible binding for global variable 'SUID'
.nodeNameToNodeSUID: no visible binding for global variable 'SUID'
commandsGET: no visible binding for global variable 'requester'
commandsHelp: no visible binding for global variable 'requester'
commandsPOST: no visible binding for global variable 'requester'
createNetworkFromDataFrames: no visible binding for global variable
'SUID'
cyrestDELETE: no visible binding for global variable 'requester'
cyrestGET: no visible binding for global variable 'requester'
cyrestPOST: no visible binding for global variable 'requester'
cyrestPUT: no visible binding for global variable 'requester'
paletteColorRandom: no visible global function definition for 'rgb'
Undefined global functions or variables:
SUID requester rgb
Consider adding
importFrom("grDevices", "rgb")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/RCy3.Rcheck/00check.log'
for details.
RCy3.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/RCy3_2.12.4.tar.gz && rm -rf RCy3.buildbin-libdir && mkdir RCy3.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCy3.buildbin-libdir RCy3_2.12.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RCy3_2.12.4.zip && rm RCy3_2.12.4.tar.gz RCy3_2.12.4.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 919k 100 919k 0 0 1617k 0 --:--:-- --:--:-- --:--:-- 1619k
install for i386
* installing *source* package 'RCy3' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RCy3'
finding HTML links ... done
AddToGroup html
RCy3 html
RemoveFromGroup html
addAnnotationText html
addCyEdges html
addCyNodes html
analyzeNetwork html
applyFilter html
bundleEdges html
checkNotebookIsRunning html
checkRunningRemote html
clearEdgeBends html
clearEdgePropertyBypass html
clearNetworkCenterBypass html
clearNetworkPropertyBypass html
clearNetworkZoomBypass html
clearNodeOpacityBypass html
clearNodePropertyBypass html
clearSelection html
cloneNetwork html
closeSession html
collapseGroup html
commandEcho html
commandOpenDialog html
commandPause html
commandQuit html
commandRunFile html
commandSleep html
commandsAPI html
commandsGET html
commandsHelp html
commandsPOST html
commandsRun html
copyVisualStyle html
createColumnFilter html
createCompositeFilter html
createDegreeFilter html
createGraphFromNetwork html
createGroup html
createGroupByColumn html
createIgraphFromNetwork html
createNetworkFromDataFrames html
createNetworkFromGraph html
createNetworkFromIgraph html
createSubnetwork html
createVisualStyle html
cybrowserClose html
cybrowserDialog html
cybrowserHide html
cybrowserList html
cybrowserSend html
cybrowserShow html
cybrowserVersion html
cyrestAPI html
cyrestDELETE html
cyrestGET html
cyrestPOST html
cyrestPUT html
cytoscapeApiVersions html
cytoscapeFreeMemory html
cytoscapeMemoryStatus html
cytoscapeNumberOfCores html
cytoscapePing html
cytoscapeVersionInfo html
deleteAllNetworks html
deleteAnnotation html
deleteDuplicateEdges html
deleteGroup html
deleteNetwork html
deleteSelectedEdges html
deleteSelectedNodes html
deleteSelfLoops html
deleteStyleMapping html
deleteTableColumn html
deleteVisualStyle html
diffusionAdvanced html
diffusionBasic html
disableApp html
doInitializeSandbox html
doRequestRemote html
doSetSandbox html
dockPanel html
dot-getDefaultSandbox html
dot-getRequester html
enableApp html
expandGroup html
exportFilters html
exportImage html
exportNetwork html
exportNetworkToNDEx html
exportVisualStyles html
findRemoteCytoscape html
fitContent html
floatPanel html
getAbsSandboxPath html
getAllEdges html
getAllNodes html
getAllStyleMappings html
getAnnotationList html
getAppInformation html
getAppStatus html
getAppUpdates html
getArrowShapes html
getAvailableApps html
getBackgroundColorDefault html
getBrowserClientChannel html
getBrowserClientJs html
getCollectionList html
getCollectionName html
getCollectionNetworks html
getCollectionSuid html
getCurrentSandbox html
getCurrentSandboxName html
getCurrentSandboxPath html
getCurrentStyle html
getDefaultSandbox html
getDefaultSandboxPath html
getDisabledApps html
getEdgeColor html
getEdgeCount html
getEdgeInfo html
getEdgeLineStyle html
getEdgeLineWidth html
getEdgeProperty html
getEdgeSelectionColorDefault html
getEdgeTargetArrowShape html
getFilterList html
getFirstNeighbors html
getGroupInfo html
getInstalledApps html
getJupyterBridgeURL html
getLayoutNameMapping html
getLayoutNames html
getLayoutPropertyNames html
getLayoutPropertyType html
getLayoutPropertyValue html
getLineStyles html
getNetworkCenter html
getNetworkCount html
getNetworkList html
getNetworkNDExId html
getNetworkName html
getNetworkProperty html
getNetworkSuid html
getNetworkViewSuid html
getNetworkViews html
getNetworkZoom html
getNodeColor html
getNodeCount html
getNodeHeight html
getNodePosition html
getNodeProperty html
getNodeSelectionColorDefault html
getNodeShapes html
getNodeSize html
getNodeWidth html
getNotebookIsRunning html
getSandboxReinitialize html
getSelectedEdgeCount html
getSelectedEdges html
getSelectedNodeCount html
getSelectedNodes html
getStyleDependencies html
getStyleMapping html
getTableColumnNames html
getTableColumnTypes html
getTableColumns html
getTableValue html
getUninstalledApps html
getVisualPropertyDefault html
getVisualPropertyNames html
getVisualStyleNames html
hideAllPanels html
hideEdges html
hideNodes html
hidePanel html
hideSelectedEdges html
hideSelectedNodes html
importFilters html
importNetworkFromFile html
importNetworkFromNDEx html
importVisualStyles html
installApp html
invertEdgeSelection html
invertNodeSelection html
layoutCopycat html
layoutNetwork html
listGroups html
loadTableData html
lockNodeDimensions html
makeSimpleGraph html
makeSimpleIgraph html
mapTableColumn html
mapVisualProperty html
matchArrowColorToEdge html
mergeNetworks html
openAppStore html
openSession html
paletteColorBrewerAccent html
paletteColorBrewerBlues html
paletteColorBrewerBrBG html
paletteColorBrewerBuGn html
paletteColorBrewerBuPu html
paletteColorBrewerDark2 html
paletteColorBrewerGnBu html
paletteColorBrewerGreens html
paletteColorBrewerGreys html
paletteColorBrewerOrRd html
paletteColorBrewerOranges html
paletteColorBrewerPRGn html
paletteColorBrewerPaired html
paletteColorBrewerPastel1 html
paletteColorBrewerPastel2 html
paletteColorBrewerPiYG html
paletteColorBrewerPuBu html
paletteColorBrewerPuBuGn html
paletteColorBrewerPuOr html
paletteColorBrewerPuRd html
paletteColorBrewerPurples html
paletteColorBrewerRdBu html
paletteColorBrewerRdPu html
paletteColorBrewerRdYlBu html
paletteColorBrewerReds html
paletteColorBrewerSet1 html
paletteColorBrewerSet2 html
paletteColorBrewerSet3 html
paletteColorBrewerYlGn html
paletteColorBrewerYlGnBu html
paletteColorBrewerYlOrBr html
paletteColorBrewerYlOrRd html
paletteColorRandom html
removeNodeCustomGraphics html
renameNetwork html
renameTableColumn html
resetDefaultSandbox html
runningRemoteCheck html
sandboxGetFileInfo html
sandboxGetFrom html
sandboxInitializer html
sandboxRemove html
sandboxRemoveFile html
sandboxSendTo html
sandboxSet html
sandboxUrlTo html
saveSession html
selectAllEdges html
selectAllNodes html
selectEdges html
selectEdgesAdjacentToSelectedNodes html
selectEdgesConnectingSelectedNodes html
selectFirstNeighbors html
selectNodes html
selectNodesConnectedBySelectedEdges html
setBackgroundColorDefault html
setCatchupFilterSecs html
setCatchupNetworkSecs html
setCurrentNetwork html
setCurrentSandbox html
setCurrentView html
setDefaultSandbox html
setDefaultSandboxPath html
setEdgeColorBypass html
setEdgeColorDefault html
setEdgeColorMapping html
setEdgeFontFaceBypass html
setEdgeFontFaceDefault html
setEdgeFontFaceMapping html
setEdgeFontSizeBypass html
setEdgeFontSizeDefault html
setEdgeFontSizeMapping html
setEdgeLabelBypass html
setEdgeLabelColorBypass html
setEdgeLabelColorDefault html
setEdgeLabelColorMapping html
setEdgeLabelDefault html
setEdgeLabelMapping html
setEdgeLabelOpacityBypass html
setEdgeLabelOpacityDefault html
setEdgeLabelOpacityMapping html
setEdgeLineStyleBypass html
setEdgeLineStyleDefault html
setEdgeLineStyleMapping html
setEdgeLineWidthBypass html
setEdgeLineWidthDefault html
setEdgeLineWidthMapping html
setEdgeOpacityBypass html
setEdgeOpacityDefault html
setEdgeOpacityMapping html
setEdgePropertyBypass html
setEdgeSelectionColorDefault html
setEdgeSourceArrowColorBypass html
setEdgeSourceArrowColorDefault html
setEdgeSourceArrowColorMapping html
setEdgeSourceArrowMapping html
setEdgeSourceArrowShapeBypass html
setEdgeSourceArrowShapeDefault html
setEdgeSourceArrowShapeMapping html
setEdgeTargetArrowColorBypass html
setEdgeTargetArrowColorDefault html
setEdgeTargetArrowColorMapping html
setEdgeTargetArrowMapping html
setEdgeTargetArrowShapeBypass html
setEdgeTargetArrowShapeDefault html
setEdgeTargetArrowShapeMapping html
setEdgeTooltipBypass html
setEdgeTooltipDefault html
setEdgeTooltipMapping html
setLayoutProperties html
setModelPropagationSecs html
setNetworkCenterBypass html
setNetworkPropertyBypass html
setNetworkZoomBypass html
setNodeBorderColorBypass html
setNodeBorderColorDefault html
setNodeBorderColorMapping html
setNodeBorderOpacityBypass html
setNodeBorderOpacityDefault html
setNodeBorderOpacityMapping html
setNodeBorderWidthBypass html
setNodeBorderWidthDefault html
setNodeBorderWidthMapping html
setNodeColorBypass html
setNodeColorDefault html
setNodeColorMapping html
setNodeComboOpacityMapping html
setNodeCustomBarChart html
setNodeCustomBoxChart html
setNodeCustomHeatMapChart html
setNodeCustomLineChart html
setNodeCustomLinearGradient html
setNodeCustomPieChart html
setNodeCustomPosition html
setNodeCustomRadialGradient html
setNodeCustomRingChart html
setNodeFillOpacityBypass html
setNodeFillOpacityDefault html
setNodeFillOpacityMapping html
setNodeFontFaceBypass html
setNodeFontFaceDefault html
setNodeFontFaceMapping html
setNodeFontSizeBypass html
setNodeFontSizeDefault html
setNodeFontSizeMapping html
setNodeHeightBypass html
setNodeHeightDefault html
setNodeHeightMapping html
setNodeLabelBypass html
setNodeLabelColorBypass html
setNodeLabelColorDefault html
setNodeLabelColorMapping html
setNodeLabelDefault html
setNodeLabelMapping html
setNodeLabelOpacityBypass html
setNodeLabelOpacityDefault html
setNodeLabelOpacityMapping html
setNodeOpacityBypass html
setNodePropertyBypass html
setNodeSelectionColorDefault html
setNodeShapeBypass html
setNodeShapeDefault html
setNodeShapeMapping html
setNodeSizeBypass html
setNodeSizeDefault html
setNodeSizeMapping html
setNodeTooltipBypass html
setNodeTooltipDefault html
setNodeTooltipMapping html
setNodeWidthBypass html
setNodeWidthDefault html
setNodeWidthMapping html
setNotebookIsRunning html
setSandboxReinitialize html
setStyleDependencies html
setVisualPropertyDefault html
setVisualStyle html
spoofResponse-class html
syncNodeCustomGraphicsSize html
toggleGraphicsDetails html
unhideAll html
unhideEdges html
unhideNodes html
uninstallApp html
updateApp html
updateNetworkInNDEx html
updateStyleDefaults html
updateStyleMapping html
** 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
install for x64
* installing *source* package 'RCy3' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCy3' as RCy3_2.12.4.zip
* DONE (RCy3)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'RCy3' successfully unpacked and MD5 sums checked
|
RCy3.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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
0.32 0.01 0.31
|
RCy3.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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
0.29 0.04 0.32
|
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RCy3.Rcheck/examples_i386/RCy3-Ex.timings
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RCy3.Rcheck/examples_x64/RCy3-Ex.timings
|