Tanja Muetze
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/RCy3 |
| Branch: RELEASE_3_6 |
| Last Commit: 67a8847 |
| Last Changed Date: 2017-10-30 12:41:08 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:14:13 -0400 (Thu, 12 Apr 2018).
| Package 1138/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RCy3 1.8.0 Tanja Muetze
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: RCy3 |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.8.0.tar.gz |
| StartedAt: 2018-04-12 02:14:29 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:15:15 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 46.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RCy3.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RCy3_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/RCy3.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.0’
* 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 ... OK
* 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
.BBSOverride: no visible global function definition for ‘as’
is.classic.graph: no visible global function definition for ‘is’
is.multiGraph: no visible global function definition for ‘is’
Undefined global functions or variables:
as is
Consider adding
importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘copyCytoscapeNetwork’ ‘renameCytoscapeNetwork’ ‘selectAllEdges’
‘selectAllNodes’
Undocumented S4 methods:
generic 'copyCytoscapeNetwork' and siglist 'CytoscapeWindowClass'
generic 'renameCytoscapeNetwork' and siglist 'CytoscapeWindowClass'
generic 'selectAllEdges' and siglist 'CytoscapeWindowClass'
generic 'selectAllNodes' and siglist 'CytoscapeWindowClass'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... 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: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/RCy3.Rcheck/00check.log’
for details.
RCy3.Rcheck/00install.out
* installing *source* package ‘RCy3’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RCy3)
RCy3.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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
0.176 0.004 0.173
RCy3.Rcheck/RCy3-Ex.timings
| name | user | system | elapsed | |
| CytoscapeConnection | 0 | 0 | 0 | |
| CytoscapeConnectionClass-class | 0.000 | 0.000 | 0.001 | |
| CytoscapeWindow | 0.000 | 0.000 | 0.001 | |
| CytoscapeWindowClass-class | 0 | 0 | 0 | |
| addCyEdge | 0.000 | 0.004 | 0.001 | |
| addCyNode | 0.000 | 0.000 | 0.001 | |
| addGraphToGraph | 0.000 | 0.000 | 0.001 | |
| clearSelection | 0.000 | 0.000 | 0.001 | |
| copyVisualStyle | 0.000 | 0.000 | 0.001 | |
| createWindow | 0.004 | 0.000 | 0.000 | |
| createWindowFromSelection | 0 | 0 | 0 | |
| cy2.edge.names | 0.000 | 0.000 | 0.001 | |
| cyPlot | 0.000 | 0.004 | 0.001 | |
| deleteAllWindows | 0 | 0 | 0 | |
| deleteEdgeAttribute | 0.000 | 0.000 | 0.001 | |
| deleteNodeAttribute | 0.004 | 0.000 | 0.001 | |
| deleteSelectedEdges | 0.000 | 0.000 | 0.001 | |
| deleteSelectedNodes | 0.000 | 0.000 | 0.001 | |
| deleteWindow | 0.000 | 0.004 | 0.000 | |
| demoSimpleGraph | 0 | 0 | 0 | |
| displayGraph | 0 | 0 | 0 | |
| dockPanel | 0.004 | 0.000 | 0.001 | |
| eda | 0.000 | 0.000 | 0.001 | |
| eda.names | 0 | 0 | 0 | |
| existing.CytoscapeWindow | 0 | 0 | 0 | |
| fitContent | 0 | 0 | 0 | |
| fitSelectedContent | 0.000 | 0.000 | 0.001 | |
| floatPanel | 0 | 0 | 0 | |
| getAdjacentEdgeNames | 0 | 0 | 0 | |
| getAllEdgeAttributes | 0.000 | 0.000 | 0.001 | |
| getAllEdges | 0.000 | 0.000 | 0.001 | |
| getAllNodeAttributes | 0 | 0 | 0 | |
| getAllNodes | 0.000 | 0.000 | 0.001 | |
| getArrowShapes | 0.000 | 0.000 | 0.001 | |
| getAttributeClassNames | 0.004 | 0.000 | 0.001 | |
| getCenter | 0 | 0 | 0 | |
| getDefaultBackgroundColor | 0.000 | 0.000 | 0.001 | |
| getDefaultEdgeReverseSelectionColor | 0.004 | 0.000 | 0.001 | |
| getDefaultEdgeSelectionColor | 0.000 | 0.000 | 0.001 | |
| getDefaultNodeReverseSelectionColor | 0 | 0 | 0 | |
| getDefaultNodeSelectionColor | 0 | 0 | 0 | |
| getDirectlyModifiableVisualProperties | 0 | 0 | 0 | |
| getEdgeAttribute | 0.000 | 0.000 | 0.001 | |
| getEdgeAttributeNames | 0 | 0 | 0 | |
| getEdgeCount | 0.000 | 0.000 | 0.001 | |
| getFirstNeighbors | 0.000 | 0.000 | 0.001 | |
| getGraph | 0 | 0 | 0 | |
| getGraphFromCyWindow | 0 | 0 | 0 | |
| getLayoutNameMapping | 0.000 | 0.000 | 0.001 | |
| getLayoutNames | 0.000 | 0.000 | 0.001 | |
| getLayoutPropertyNames | 0.004 | 0.000 | 0.000 | |
| getLayoutPropertyType | 0.000 | 0.000 | 0.001 | |
| getLayoutPropertyValue | 0.000 | 0.000 | 0.001 | |
| getLineStyles | 0 | 0 | 0 | |
| getNodeAttribute | 0 | 0 | 0 | |
| getNodeAttributeNames | 0.000 | 0.000 | 0.001 | |
| getNodeCount | 0.004 | 0.000 | 0.001 | |
| getNodePosition | 0 | 0 | 0 | |
| getNodeShapes | 0 | 0 | 0 | |
| getNodeSize | 0.000 | 0.004 | 0.001 | |
| getSelectedEdgeCount | 0 | 0 | 0 | |
| getSelectedEdges | 0.000 | 0.000 | 0.001 | |
| getSelectedNodeCount | 0.004 | 0.000 | 0.001 | |
| getSelectedNodes | 0.000 | 0.000 | 0.001 | |
| getViewCoordinates | 0.000 | 0.000 | 0.001 | |
| getVisualStyleNames | 0 | 0 | 0 | |
| getWindowCount | 0 | 0 | 0 | |
| getWindowID | 0.000 | 0.000 | 0.001 | |
| getWindowList | 0.004 | 0.000 | 0.000 | |
| getZoom | 0 | 0 | 0 | |
| hideAllPanels | 0.000 | 0.000 | 0.001 | |
| hideNodes | 0.004 | 0.000 | 0.001 | |
| hidePanel | 0 | 0 | 0 | |
| hideSelectedEdges | 0.000 | 0.000 | 0.001 | |
| hideSelectedNodes | 0.004 | 0.000 | 0.001 | |
| initEdgeAttribute | 0 | 0 | 0 | |
| initNodeAttribute | 0 | 0 | 0 | |
| invertEdgeSelection | 0.004 | 0.000 | 0.001 | |
| invertNodeSelection | 0.000 | 0.000 | 0.001 | |
| layoutNetwork | 0 | 0 | 0 | |
| lockNodeDimensions | 0.004 | 0.000 | 0.001 | |
| makeRandomGraph | 0.000 | 0.000 | 0.002 | |
| makeSimpleGraph | 0.004 | 0.000 | 0.002 | |
| noa | 0.000 | 0.000 | 0.001 | |
| noa.names | 0 | 0 | 0 | |
| ping | 0 | 0 | 0 | |
| pluginVersion | 0.000 | 0.000 | 0.001 | |
| predictTimeToDisplayGraph | 0.000 | 0.000 | 0.001 | |
| raiseWindow | 0 | 0 | 0 | |
| redraw | 0 | 0 | 0 | |
| restoreLayout | 0 | 0 | 0 | |
| saveImage | 0.000 | 0.000 | 0.001 | |
| saveLayout | 0.000 | 0.000 | 0.001 | |
| saveNetwork | 0 | 0 | 0 | |
| selectEdges | 0 | 0 | 0 | |
| selectFirstNeighborsOfSelectedNodes | 0.000 | 0.000 | 0.001 | |
| selectNodes | 0 | 0 | 0 | |
| sendEdges | 0 | 0 | 0 | |
| sendNodes | 0 | 0 | 0 | |
| setCenter | 0.000 | 0.000 | 0.001 | |
| setDefaultBackgroundColor | 0.000 | 0.004 | 0.001 | |
| setDefaultEdgeColor | 0 | 0 | 0 | |
| setDefaultEdgeFontSize | 0 | 0 | 0 | |
| setDefaultEdgeLineWidth | 0.004 | 0.000 | 0.001 | |
| setDefaultEdgeReverseSelectionColor | 0.000 | 0.000 | 0.001 | |
| setDefaultEdgeSelectionColor | 0 | 0 | 0 | |
| setDefaultEdgeSourceArrowColor | 0.000 | 0.000 | 0.001 | |
| setDefaultEdgeTargetArrowColor | 0.000 | 0.000 | 0.001 | |
| setDefaultNodeBorderColor | 0.000 | 0.000 | 0.001 | |
| setDefaultNodeBorderWidth | 0.004 | 0.000 | 0.001 | |
| setDefaultNodeColor | 0 | 0 | 0 | |
| setDefaultNodeFontSize | 0 | 0 | 0 | |
| setDefaultNodeLabelColor | 0.000 | 0.004 | 0.001 | |
| setDefaultNodeReverseSelectionColor | 0.000 | 0.000 | 0.001 | |
| setDefaultNodeSelectionColor | 0 | 0 | 0 | |
| setDefaultNodeShape | 0.000 | 0.000 | 0.001 | |
| setDefaultNodeSize | 0 | 0 | 0 | |
| setEdgeAttributes | 0 | 0 | 0 | |
| setEdgeAttributesDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeColorDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeColorRule | 0.004 | 0.000 | 0.000 | |
| setEdgeFontSizeDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeLabelColorDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeLabelDirect | 0 | 0 | 0 | |
| setEdgeLabelOpacityDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeLabelRule | 0 | 0 | 0 | |
| setEdgeLineStyleDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeLineStyleRule | 0 | 0 | 0 | |
| setEdgeLineWidthDirect | 0 | 0 | 0 | |
| setEdgeLineWidthRule | 0.000 | 0.000 | 0.001 | |
| setEdgeOpacityDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeOpacityRule | 0.000 | 0.000 | 0.001 | |
| setEdgeSourceArrowColorDirect | 0.000 | 0.000 | 0.002 | |
| setEdgeSourceArrowColorRule | 0.000 | 0.000 | 0.001 | |
| setEdgeSourceArrowOpacityDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeSourceArrowRule | 0 | 0 | 0 | |
| setEdgeSourceArrowShapeDirect | 0.004 | 0.000 | 0.001 | |
| setEdgeTargetArrowColorDirect | 0.000 | 0.000 | 0.001 | |
| setEdgeTargetArrowColorRule | 0.000 | 0.000 | 0.001 | |
| setEdgeTargetArrowOpacityDirect | 0.004 | 0.000 | 0.000 | |
| setEdgeTargetArrowRule | 0 | 0 | 0 | |
| setEdgeTargetArrowShapeDirect | 0.004 | 0.000 | 0.001 | |
| setEdgeTooltipDirect | 0 | 0 | 0 | |
| setEdgeTooltipRule | 0.000 | 0.000 | 0.001 | |
| setGraph | 0.004 | 0.000 | 0.001 | |
| setLayoutProperties | 0 | 0 | 0 | |
| setNodeAttributes | 0.000 | 0.000 | 0.001 | |
| setNodeAttributesDirect | 0.004 | 0.000 | 0.001 | |
| setNodeBorderColorDirect | 0.000 | 0.000 | 0.001 | |
| setNodeBorderColorRule | 0.000 | 0.000 | 0.001 | |
| setNodeBorderOpacityDirect | 0 | 0 | 0 | |
| setNodeBorderWidthDirect | 0.000 | 0.000 | 0.001 | |
| setNodeBorderWidthRule | 0.000 | 0.000 | 0.001 | |
| setNodeColorDirect | 0 | 0 | 0 | |
| setNodeColorRule | 0.000 | 0.000 | 0.001 | |
| setNodeFillOpacityDirect | 0.000 | 0.000 | 0.001 | |
| setNodeFontSizeDirect | 0 | 0 | 0 | |
| setNodeHeightDirect | 0.000 | 0.000 | 0.001 | |
| setNodeImageDirect | 0 | 0 | 0 | |
| setNodeLabelColorDirect | 0.000 | 0.000 | 0.001 | |
| setNodeLabelDirect | 0.000 | 0.000 | 0.001 | |
| setNodeLabelOpacityDirect | 0 | 0 | 0 | |
| setNodeLabelRule | 0 | 0 | 0 | |
| setNodeOpacityDirect | 0.000 | 0.000 | 0.001 | |
| setNodeOpacityRule | 0.000 | 0.000 | 0.001 | |
| setNodePosition | 0 | 0 | 0 | |
| setNodeShapeDirect | 0.000 | 0.000 | 0.001 | |
| setNodeShapeRule | 0 | 0 | 0 | |
| setNodeSizeDirect | 0 | 0 | 0 | |
| setNodeSizeRule | 0.000 | 0.000 | 0.001 | |
| setNodeTooltipRule | 0 | 0 | 0 | |
| setNodeWidthDirect | 0.000 | 0.000 | 0.001 | |
| setTooltipDismissDelay | 0.000 | 0.000 | 0.001 | |
| setTooltipInitialDelay | 0.000 | 0.000 | 0.001 | |
| setVisualStyle | 0.000 | 0.000 | 0.001 | |
| setWindowSize | 0 | 0 | 0 | |
| setZoom | 0.004 | 0.000 | 0.001 | |
| showGraphicsDetails | 0.000 | 0.000 | 0.001 | |
| unhideAll | 0 | 0 | 0 | |