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CHECK report for RCy3 on malbec1

This page was generated on 2019-04-16 11:51:40 -0400 (Tue, 16 Apr 2019).

Package 1269/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.2.9
Alexander Pico , Tanja Muetze , Paul Shannon
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RCy3
Branch: RELEASE_3_8
Last Commit: 0578a69
Last Changed Date: 2019-03-07 21:24:24 -0400 (Thu, 07 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCy3
Version: 2.2.9
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RCy3_2.2.9.tar.gz
StartedAt: 2019-04-16 02:26:55 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:28:03 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 67.5 seconds
RetCode: 0
Status:  OK 
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RCy3_2.2.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RCy3.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘2.2.9’
* 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 ... 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
* 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
createNetworkFromDataFrames: no visible binding for global variable
  ‘SUID’
Undefined global functions or variables:
  SUID
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/RCy3.Rcheck/00check.log’
for details.



Installation output

RCy3.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘RCy3’ ...
** 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
* DONE (RCy3)

Tests output

RCy3.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.216   0.016   0.255 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
AddToGroup000
RemoveFromGroup0.0040.0000.000
addCyEdges000
addCyNodes0.0000.0000.001
applyFilter000
bundleEdges000
clearEdgePropertyBypass000
clearNetworkCenterBypass0.0000.0000.001
clearNetworkPropertyBypass000
clearNetworkZoomBypass000
clearNodeOpacityBypass000
clearNodePropertyBypass000
clearSelection000
cloneNetwork000
closeSession000
collapseGroup000
commandEcho000
commandOpenDialog000
commandPause000
commandQuit000
commandRunFile000
commandSleep000
commandsAPI000
commandsGET000
commandsHelp000
commandsPOST000
commandsRun000
copyVisualStyle000
createColumnFilter000
createCompositeFilter000
createDegreeFilter000
createGraphFromNetwork000
createGroup000
createIgraphFromNetwork000
createNetworkFromDataFrames000
createNetworkFromGraph000
createNetworkFromIgraph0.0000.0000.001
createSubnetwork000
createVisualStyle000
cybrowserClose000
cybrowserDialog0.0000.0000.001
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow0.0000.0000.001
cybrowserVersion000
cyrestAPI000
cyrestDELETE000
cyrestGET0.0000.0000.001
cyrestPOST000
cyrestPUT000
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus0.0040.0000.000
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks0.0000.0000.001
deleteDuplicateEdges000
deleteGroup000
deleteNetwork000
deleteSelectedEdges0.0000.0000.001
deleteSelectedNodes000
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle000
diffusionAdvanced000
diffusionBasic000
disableApp000
dockPanel000
enableApp000
expandGroup000
exportFilters000
exportImage000
exportNetwork0.0000.0000.001
exportNetworkToNDEx000
exportVisualStyles000
fitContent000
floatPanel000
getAllEdges000
getAllNodes000
getAppInformation000
getAppStatus0.0000.0000.001
getAppUpdates000
getArrowShapes000
getAvailableApps000
getBackgroundColorDefault0.0000.0000.001
getCollectionList000
getCollectionName000
getCollectionNetworks0.0040.0000.000
getCollectionSuid000
getDisabledApps000
getEdgeColor0.0000.0000.001
getEdgeCount000
getEdgeLineStyle000
getEdgeLineWidth0.0040.0000.000
getEdgeProperty000
getEdgeSelectionColorDefault0.0000.0000.001
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo000
getInstalledApps000
getLayoutNameMapping0.0000.0000.001
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType000
getLayoutPropertyValue000
getLineStyles000
getNetworkCenter000
getNetworkCount000
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom0.0000.0040.000
getNodeColor000
getNodeCount000
getNodeHeight000
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize0.0000.0000.001
getNodeWidth000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes000
getStyleDependencies000
getTableColumnNames000
getTableColumnTypes000
getTableColumns0.0000.0000.001
getTableValue000
getUninstalledApps000
getVisualPropertyDefault000
getVisualPropertyNames000
getVisualStyleNames000
hideAllPanels0.0000.0000.001
hideEdges000
hideNodes000
hidePanel000
hideSelectedEdges000
hideSelectedNodes000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx000
importVisualStyles000
installApp000
invertEdgeSelection000
invertNodeSelection0.0000.0000.001
layoutCopycat000
layoutNetwork000
listGroups000
lockNodeDimensions000
makeSimpleGraph0.0840.0000.088
makeSimpleIgraph0.0160.0000.016
mapTableColumn0.0000.0000.001
mapVisualProperty000
matchArrowColorToEdge000
openAppStore000
openSession000
removeNodeCustomGraphics000
renameNetwork000
renameTableColumn000
saveSession000
selectAllEdges000
selectAllNodes0.0000.0000.001
selectEdges000
selectEdgesAdjacentToSelectedNodes000
selectEdgesConnectingSelectedNodes000
selectFirstNeighbors000
selectNodes000
selectNodesConnectedBySelectedEdges000
setBackgroundColorDefault000
setCurrentNetwork000
setCurrentView000
setEdgeColorBypass0.0040.0000.000
setEdgeColorDefault0.0000.0000.001
setEdgeColorMapping0.0000.0000.001
setEdgeFontFaceBypass000
setEdgeFontSizeBypass000
setEdgeFontSizeDefault000
setEdgeLabelBypass000
setEdgeLabelColorBypass000
setEdgeLabelMapping000
setEdgeLabelOpacityBypass000
setEdgeLineStyleBypass000
setEdgeLineStyleDefault000
setEdgeLineStyleMapping000
setEdgeLineWidthBypass000
setEdgeLineWidthDefault000
setEdgeLineWidthMapping000
setEdgeOpacityBypass000
setEdgeOpacityMapping0.0000.0000.001
setEdgePropertyBypass000
setEdgeSelectionColorDefault000
setEdgeSourceArrowColorBypass000
setEdgeSourceArrowColorDefault0.0000.0000.001
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass000
setEdgeSourceArrowShapeDefault000
setEdgeTargetArrowColorBypass000
setEdgeTargetArrowColorDefault000
setEdgeTargetArrowColorMapping000
setEdgeTargetArrowMapping000
setEdgeTargetArrowShapeBypass0.0000.0040.001
setEdgeTargetArrowShapeDefault000
setEdgeTooltipBypass000
setEdgeTooltipMapping0.0000.0000.001
setLayoutProperties000
setNetworkCenterBypass000
setNetworkPropertyBypass000
setNetworkZoomBypass000
setNodeBorderColorBypass000
setNodeBorderColorDefault000
setNodeBorderColorMapping000
setNodeBorderOpacityBypass000
setNodeBorderWidthBypass000
setNodeBorderWidthDefault0.0000.0000.001
setNodeBorderWidthMapping000
setNodeColorBypass0.0000.0000.001
setNodeColorDefault000
setNodeColorMapping000
setNodeComboOpacityMapping000
setNodeCustomBarChart000
setNodeCustomBoxChart0.0000.0000.001
setNodeCustomHeatMapChart000
setNodeCustomLineChart000
setNodeCustomLinearGradient000
setNodeCustomPieChart000
setNodeCustomPosition000
setNodeCustomRadialGradient000
setNodeCustomRingChart000
setNodeFillOpacityBypass000
setNodeFontSizeBypass000
setNodeFontSizeDefault000
setNodeHeightBypass000
setNodeLabelBypass000
setNodeLabelColorBypass000
setNodeLabelColorDefault0.0000.0000.001
setNodeLabelMapping000
setNodeLabelOpacityBypass000
setNodeOpacityBypass000
setNodePropertyBypass000
setNodeSelectionColorDefault000
setNodeShapeBypass000
setNodeShapeDefault0.0000.0000.001
setNodeShapeMapping000
setNodeSizeBypass000
setNodeSizeDefault000
setNodeSizeMapping000
setNodeTooltipMapping000
setNodeWidthBypass000
setStyleDependencies000
setVisualPropertyDefault000
setVisualStyle000
syncNodeCustomGraphicsSize0.0000.0000.001
toggleGraphicsDetails000
unhideAll000
unhideEdges0.0000.0000.001
unhideNodes000
uninstallApp000
updateApp000
updateNetworkInNDEx000
updateStyleDefaults000
updateStyleMapping000