Alexander Pico
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RCy3 |
| Branch: master |
| Last Commit: 0d8c8b0 |
| Last Changed Date: 2019-03-30 14:56:28 -0400 (Sat, 30 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:44:03 -0400 (Tue, 09 Apr 2019).
| Package 1308/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RCy3 2.3.12 Alexander Pico
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: RCy3 |
| Version: 2.3.12 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RCy3_2.3.12.tar.gz |
| StartedAt: 2019-04-09 03:05:57 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:07:03 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 66.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RCy3.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RCy3_2.3.12.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RCy3.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * 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 ‘2.3.12’ * 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-3.9-bioc/meat/RCy3.Rcheck/00check.log’ for details.
RCy3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RCy3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)
RCy3.Rcheck/tests/runTests.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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
0.171 0.027 0.185
RCy3.Rcheck/RCy3-Ex.timings
| name | user | system | elapsed | |
| AddToGroup | 0.001 | 0.000 | 0.000 | |
| RemoveFromGroup | 0 | 0 | 0 | |
| addCyEdges | 0 | 0 | 0 | |
| addCyNodes | 0 | 0 | 0 | |
| applyFilter | 0 | 0 | 0 | |
| bundleEdges | 0 | 0 | 0 | |
| clearEdgePropertyBypass | 0 | 0 | 0 | |
| clearNetworkCenterBypass | 0 | 0 | 0 | |
| clearNetworkPropertyBypass | 0 | 0 | 0 | |
| clearNetworkZoomBypass | 0 | 0 | 0 | |
| clearNodeOpacityBypass | 0 | 0 | 0 | |
| clearNodePropertyBypass | 0 | 0 | 0 | |
| clearSelection | 0.001 | 0.000 | 0.000 | |
| cloneNetwork | 0 | 0 | 0 | |
| closeSession | 0.001 | 0.000 | 0.000 | |
| collapseGroup | 0 | 0 | 0 | |
| commandEcho | 0 | 0 | 0 | |
| commandOpenDialog | 0 | 0 | 0 | |
| commandPause | 0 | 0 | 0 | |
| commandQuit | 0 | 0 | 0 | |
| commandRunFile | 0 | 0 | 0 | |
| commandSleep | 0 | 0 | 0 | |
| commandsAPI | 0 | 0 | 0 | |
| commandsGET | 0.000 | 0.000 | 0.001 | |
| commandsHelp | 0 | 0 | 0 | |
| commandsPOST | 0.000 | 0.000 | 0.001 | |
| commandsRun | 0 | 0 | 0 | |
| copyVisualStyle | 0.000 | 0.001 | 0.000 | |
| createColumnFilter | 0 | 0 | 0 | |
| createCompositeFilter | 0.000 | 0.001 | 0.000 | |
| createDegreeFilter | 0 | 0 | 0 | |
| createGraphFromNetwork | 0 | 0 | 0 | |
| createGroup | 0 | 0 | 0 | |
| createIgraphFromNetwork | 0 | 0 | 0 | |
| createNetworkFromDataFrames | 0 | 0 | 0 | |
| createNetworkFromGraph | 0 | 0 | 0 | |
| createNetworkFromIgraph | 0 | 0 | 0 | |
| createSubnetwork | 0 | 0 | 0 | |
| createVisualStyle | 0 | 0 | 0 | |
| cybrowserClose | 0.001 | 0.000 | 0.000 | |
| cybrowserDialog | 0 | 0 | 0 | |
| cybrowserHide | 0 | 0 | 0 | |
| cybrowserList | 0 | 0 | 0 | |
| cybrowserSend | 0 | 0 | 0 | |
| cybrowserShow | 0 | 0 | 0 | |
| cybrowserVersion | 0.000 | 0.000 | 0.001 | |
| cyrestAPI | 0 | 0 | 0 | |
| cyrestDELETE | 0.000 | 0.000 | 0.001 | |
| cyrestGET | 0 | 0 | 0 | |
| cyrestPOST | 0 | 0 | 0 | |
| cyrestPUT | 0 | 0 | 0 | |
| cytoscapeApiVersions | 0 | 0 | 0 | |
| cytoscapeFreeMemory | 0 | 0 | 0 | |
| cytoscapeMemoryStatus | 0.000 | 0.000 | 0.001 | |
| cytoscapeNumberOfCores | 0 | 0 | 0 | |
| cytoscapePing | 0.000 | 0.000 | 0.001 | |
| cytoscapeVersionInfo | 0 | 0 | 0 | |
| deleteAllNetworks | 0.000 | 0.000 | 0.001 | |
| deleteDuplicateEdges | 0 | 0 | 0 | |
| deleteGroup | 0.000 | 0.000 | 0.001 | |
| deleteNetwork | 0 | 0 | 0 | |
| deleteSelectedEdges | 0 | 0 | 0 | |
| deleteSelectedNodes | 0 | 0 | 0 | |
| deleteSelfLoops | 0 | 0 | 0 | |
| deleteStyleMapping | 0 | 0 | 0 | |
| deleteTableColumn | 0 | 0 | 0 | |
| deleteVisualStyle | 0 | 0 | 0 | |
| diffusionAdvanced | 0 | 0 | 0 | |
| diffusionBasic | 0 | 0 | 0 | |
| disableApp | 0 | 0 | 0 | |
| dockPanel | 0 | 0 | 0 | |
| enableApp | 0.001 | 0.000 | 0.000 | |
| expandGroup | 0 | 0 | 0 | |
| exportFilters | 0.001 | 0.000 | 0.000 | |
| exportImage | 0 | 0 | 0 | |
| exportNetwork | 0.001 | 0.000 | 0.000 | |
| exportNetworkToNDEx | 0 | 0 | 0 | |
| exportVisualStyles | 0 | 0 | 0 | |
| fitContent | 0 | 0 | 0 | |
| floatPanel | 0 | 0 | 0 | |
| getAllEdges | 0 | 0 | 0 | |
| getAllNodes | 0 | 0 | 0 | |
| getAppInformation | 0 | 0 | 0 | |
| getAppStatus | 0 | 0 | 0 | |
| getAppUpdates | 0 | 0 | 0 | |
| getArrowShapes | 0 | 0 | 0 | |
| getAvailableApps | 0 | 0 | 0 | |
| getBackgroundColorDefault | 0 | 0 | 0 | |
| getCollectionList | 0.000 | 0.000 | 0.001 | |
| getCollectionName | 0 | 0 | 0 | |
| getCollectionNetworks | 0.000 | 0.000 | 0.001 | |
| getCollectionSuid | 0 | 0 | 0 | |
| getDisabledApps | 0 | 0 | 0 | |
| getEdgeColor | 0 | 0 | 0 | |
| getEdgeCount | 0 | 0 | 0 | |
| getEdgeLineStyle | 0 | 0 | 0 | |
| getEdgeLineWidth | 0 | 0 | 0 | |
| getEdgeProperty | 0 | 0 | 0 | |
| getEdgeSelectionColorDefault | 0 | 0 | 0 | |
| getEdgeTargetArrowShape | 0 | 0 | 0 | |
| getFilterList | 0.001 | 0.000 | 0.000 | |
| getFirstNeighbors | 0 | 0 | 0 | |
| getGroupInfo | 0 | 0 | 0 | |
| getInstalledApps | 0 | 0 | 0 | |
| getLayoutNameMapping | 0 | 0 | 0 | |
| getLayoutNames | 0 | 0 | 0 | |
| getLayoutPropertyNames | 0 | 0 | 0 | |
| getLayoutPropertyType | 0 | 0 | 0 | |
| getLayoutPropertyValue | 0 | 0 | 0 | |
| getLineStyles | 0 | 0 | 0 | |
| getNetworkCenter | 0 | 0 | 0 | |
| getNetworkCount | 0 | 0 | 0 | |
| getNetworkList | 0 | 0 | 0 | |
| getNetworkNDExId | 0 | 0 | 0 | |
| getNetworkName | 0 | 0 | 0 | |
| getNetworkProperty | 0.000 | 0.000 | 0.001 | |
| getNetworkSuid | 0 | 0 | 0 | |
| getNetworkViewSuid | 0.000 | 0.000 | 0.001 | |
| getNetworkViews | 0 | 0 | 0 | |
| getNetworkZoom | 0.000 | 0.001 | 0.000 | |
| getNodeColor | 0 | 0 | 0 | |
| getNodeCount | 0.000 | 0.001 | 0.000 | |
| getNodeHeight | 0 | 0 | 0 | |
| getNodeProperty | 0 | 0 | 0 | |
| getNodeSelectionColorDefault | 0 | 0 | 0 | |
| getNodeShapes | 0 | 0 | 0 | |
| getNodeSize | 0 | 0 | 0 | |
| getNodeWidth | 0 | 0 | 0 | |
| getSelectedEdgeCount | 0 | 0 | 0 | |
| getSelectedEdges | 0.001 | 0.000 | 0.000 | |
| getSelectedNodeCount | 0 | 0 | 0 | |
| getSelectedNodes | 0.001 | 0.000 | 0.000 | |
| getStyleDependencies | 0 | 0 | 0 | |
| getTableColumnNames | 0 | 0 | 0 | |
| getTableColumnTypes | 0 | 0 | 0 | |
| getTableColumns | 0 | 0 | 0 | |
| getTableValue | 0 | 0 | 0 | |
| getUninstalledApps | 0 | 0 | 0 | |
| getVisualPropertyDefault | 0 | 0 | 0 | |
| getVisualPropertyNames | 0 | 0 | 0 | |
| getVisualStyleNames | 0 | 0 | 0 | |
| hideAllPanels | 0 | 0 | 0 | |
| hideEdges | 0 | 0 | 0 | |
| hideNodes | 0 | 0 | 0 | |
| hidePanel | 0.000 | 0.000 | 0.001 | |
| hideSelectedEdges | 0 | 0 | 0 | |
| hideSelectedNodes | 0 | 0 | 0 | |
| importFilters | 0 | 0 | 0 | |
| importNetworkFromFile | 0 | 0 | 0 | |
| importNetworkFromNDEx | 0 | 0 | 0 | |
| importVisualStyles | 0 | 0 | 0 | |
| installApp | 0 | 0 | 0 | |
| invertEdgeSelection | 0 | 0 | 0 | |
| invertNodeSelection | 0 | 0 | 0 | |
| layoutCopycat | 0 | 0 | 0 | |
| layoutNetwork | 0 | 0 | 0 | |
| listGroups | 0.001 | 0.000 | 0.000 | |
| lockNodeDimensions | 0 | 0 | 0 | |
| makeSimpleGraph | 0.065 | 0.000 | 0.065 | |
| makeSimpleIgraph | 0.009 | 0.000 | 0.009 | |
| mapTableColumn | 0 | 0 | 0 | |
| mapVisualProperty | 0.000 | 0.000 | 0.001 | |
| matchArrowColorToEdge | 0 | 0 | 0 | |
| openAppStore | 0 | 0 | 0 | |
| openSession | 0 | 0 | 0 | |
| removeNodeCustomGraphics | 0 | 0 | 0 | |
| renameNetwork | 0 | 0 | 0 | |
| renameTableColumn | 0 | 0 | 0 | |
| saveSession | 0 | 0 | 0 | |
| selectAllEdges | 0 | 0 | 0 | |
| selectAllNodes | 0 | 0 | 0 | |
| selectEdges | 0 | 0 | 0 | |
| selectEdgesAdjacentToSelectedNodes | 0 | 0 | 0 | |
| selectEdgesConnectingSelectedNodes | 0.001 | 0.000 | 0.000 | |
| selectFirstNeighbors | 0 | 0 | 0 | |
| selectNodes | 0.001 | 0.000 | 0.000 | |
| selectNodesConnectedBySelectedEdges | 0 | 0 | 0 | |
| setBackgroundColorDefault | 0 | 0 | 0 | |
| setCurrentNetwork | 0 | 0 | 0 | |
| setCurrentView | 0 | 0 | 0 | |
| setEdgeColorBypass | 0 | 0 | 0 | |
| setEdgeColorDefault | 0 | 0 | 0 | |
| setEdgeColorMapping | 0 | 0 | 0 | |
| setEdgeFontFaceBypass | 0 | 0 | 0 | |
| setEdgeFontSizeBypass | 0 | 0 | 0 | |
| setEdgeFontSizeDefault | 0 | 0 | 0 | |
| setEdgeLabelBypass | 0.000 | 0.000 | 0.001 | |
| setEdgeLabelColorBypass | 0 | 0 | 0 | |
| setEdgeLabelMapping | 0.000 | 0.000 | 0.001 | |
| setEdgeLabelOpacityBypass | 0 | 0 | 0 | |
| setEdgeLineStyleBypass | 0 | 0 | 0 | |
| setEdgeLineStyleDefault | 0 | 0 | 0 | |
| setEdgeLineStyleMapping | 0 | 0 | 0 | |
| setEdgeLineWidthBypass | 0 | 0 | 0 | |
| setEdgeLineWidthDefault | 0 | 0 | 0 | |
| setEdgeLineWidthMapping | 0 | 0 | 0 | |
| setEdgeOpacityBypass | 0.001 | 0.000 | 0.000 | |
| setEdgeOpacityMapping | 0 | 0 | 0 | |
| setEdgePropertyBypass | 0.001 | 0.000 | 0.000 | |
| setEdgeSelectionColorDefault | 0 | 0 | 0 | |
| setEdgeSourceArrowColorBypass | 0 | 0 | 0 | |
| setEdgeSourceArrowColorDefault | 0 | 0 | 0 | |
| setEdgeSourceArrowColorMapping | 0 | 0 | 0 | |
| setEdgeSourceArrowMapping | 0 | 0 | 0 | |
| setEdgeSourceArrowShapeBypass | 0 | 0 | 0 | |
| setEdgeSourceArrowShapeDefault | 0 | 0 | 0 | |
| setEdgeTargetArrowColorBypass | 0 | 0 | 0 | |
| setEdgeTargetArrowColorDefault | 0.000 | 0.000 | 0.001 | |
| setEdgeTargetArrowColorMapping | 0 | 0 | 0 | |
| setEdgeTargetArrowMapping | 0.000 | 0.000 | 0.001 | |
| setEdgeTargetArrowShapeBypass | 0 | 0 | 0 | |
| setEdgeTargetArrowShapeDefault | 0.000 | 0.000 | 0.001 | |
| setEdgeTooltipBypass | 0 | 0 | 0 | |
| setEdgeTooltipMapping | 0 | 0 | 0 | |
| setLayoutProperties | 0 | 0 | 0 | |
| setNetworkCenterBypass | 0 | 0 | 0 | |
| setNetworkPropertyBypass | 0 | 0 | 0 | |
| setNetworkZoomBypass | 0 | 0 | 0 | |
| setNodeBorderColorBypass | 0 | 0 | 0 | |
| setNodeBorderColorDefault | 0 | 0 | 0 | |
| setNodeBorderColorMapping | 0 | 0 | 0 | |
| setNodeBorderOpacityBypass | 0 | 0 | 0 | |
| setNodeBorderWidthBypass | 0 | 0 | 0 | |
| setNodeBorderWidthDefault | 0 | 0 | 0 | |
| setNodeBorderWidthMapping | 0 | 0 | 0 | |
| setNodeColorBypass | 0.000 | 0.000 | 0.001 | |
| setNodeColorDefault | 0 | 0 | 0 | |
| setNodeColorMapping | 0.000 | 0.000 | 0.001 | |
| setNodeComboOpacityMapping | 0 | 0 | 0 | |
| setNodeCustomBarChart | 0 | 0 | 0 | |
| setNodeCustomBoxChart | 0 | 0 | 0 | |
| setNodeCustomHeatMapChart | 0 | 0 | 0 | |
| setNodeCustomLineChart | 0 | 0 | 0 | |
| setNodeCustomLinearGradient | 0 | 0 | 0 | |
| setNodeCustomPieChart | 0 | 0 | 0 | |
| setNodeCustomPosition | 0 | 0 | 0 | |
| setNodeCustomRadialGradient | 0 | 0 | 0 | |
| setNodeCustomRingChart | 0.001 | 0.000 | 0.000 | |
| setNodeFillOpacityBypass | 0 | 0 | 0 | |
| setNodeFontSizeBypass | 0.001 | 0.000 | 0.000 | |
| setNodeFontSizeDefault | 0 | 0 | 0 | |
| setNodeHeightBypass | 0 | 0 | 0 | |
| setNodeLabelBypass | 0 | 0 | 0 | |
| setNodeLabelColorBypass | 0 | 0 | 0 | |
| setNodeLabelColorDefault | 0 | 0 | 0 | |
| setNodeLabelMapping | 0 | 0 | 0 | |
| setNodeLabelOpacityBypass | 0 | 0 | 0 | |
| setNodeOpacityBypass | 0 | 0 | 0 | |
| setNodePropertyBypass | 0 | 0 | 0 | |
| setNodeSelectionColorDefault | 0 | 0 | 0 | |
| setNodeShapeBypass | 0 | 0 | 0 | |
| setNodeShapeDefault | 0 | 0 | 0 | |
| setNodeShapeMapping | 0.000 | 0.000 | 0.001 | |
| setNodeSizeBypass | 0 | 0 | 0 | |
| setNodeSizeDefault | 0 | 0 | 0 | |
| setNodeSizeMapping | 0 | 0 | 0 | |
| setNodeTooltipMapping | 0 | 0 | 0 | |
| setNodeWidthBypass | 0 | 0 | 0 | |
| setStyleDependencies | 0 | 0 | 0 | |
| setVisualPropertyDefault | 0 | 0 | 0 | |
| setVisualStyle | 0.000 | 0.000 | 0.001 | |
| syncNodeCustomGraphicsSize | 0.001 | 0.000 | 0.000 | |
| toggleGraphicsDetails | 0 | 0 | 0 | |
| unhideAll | 0 | 0 | 0 | |
| unhideEdges | 0 | 0 | 0 | |
| unhideNodes | 0 | 0 | 0 | |
| uninstallApp | 0 | 0 | 0 | |
| updateApp | 0 | 0 | 0 | |
| updateNetworkInNDEx | 0 | 0 | 0 | |
| updateStyleDefaults | 0 | 0 | 0 | |
| updateStyleMapping | 0 | 0 | 0 | |