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This page was generated on 2021-06-17 02:38:28 -0400 (Thu, 17 Jun 2021).

CHECK results for RCyjs on nebbiolo1

To the developers/maintainers of the RCyjs package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCyjs.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.

raw results

Package 1527/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.14.0  (landing page)
Paul Shannon
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/RCyjs
Branch: RELEASE_3_13
Last Commit: d93cc23
Last Changed Date: 2021-05-19 12:13:00 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RCyjs
Version: 2.14.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RCyjs_2.14.0.tar.gz
StartedAt: 2021-06-15 13:14:55 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 13:15:28 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 32.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RCyjs.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RCyjs_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RCyjs.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCyjs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCyjs’ version ‘2.14.0’
* 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 ‘RCyjs’ 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 ... OK
* 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 ... WARNING
Undocumented arguments in documentation object 'hideNodes,RCyjs-method'
  ‘nodeIDs’

Undocumented arguments in documentation object 'readAndStandardizeJSONNetworkFile'
  ‘filename’
Documented arguments not in \usage in documentation object 'readAndStandardizeJSONNetworkFile':
  ‘file’

Undocumented arguments in documentation object 'readAndStandardizeJSONStyleFile'
  ‘filename’
Documented arguments not in \usage in documentation object 'readAndStandardizeJSONStyleFile':
  ‘file’

Undocumented arguments in documentation object 'showNodes,RCyjs-method'
  ‘nodeIDs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking include directives in Makefiles ... 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
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/RCyjs.Rcheck/00check.log’
for details.



Installation output

RCyjs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RCyjs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘RCyjs’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘layout’ in package ‘RCyjs’
** 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 (RCyjs)

Tests output

RCyjs.Rcheck/tests/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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.

> # disabled: the bioc build system no longer supports browser use.
> # BiocGenerics:::testPackage("RCyjs")
> 
> proc.time()
   user  system elapsed 
  0.189   0.035   0.209 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class000
addGraph000
addGraphFromFile0.0010.0000.001
clearSelection0.0010.0000.001
createTestGaph0.0070.0000.007
deleteGraph0.0010.0000.001
deleteSelectedNodes0.0000.0000.001
eda000
edaNames0.0000.0010.000
fit000
fitSelection0.0000.0000.001
getEdgeCount0.0000.0000.001
getJSON000
getLayoutStrategies000
getNodeCount0.0000.0000.001
getNodes000
getPosition000
getSelectedNodes0.0010.0000.000
getSupportedEdgeDecoratorShapes0.0010.0000.000
getSupportedNodeShapes0.0000.0000.001
getZoom000
graphNELtoJSON.string000
hAlign0.0000.0010.000
hideAllEdges000
hideEdges0.0000.0000.001
hideNodes0.0000.0010.001
hideSelectedNodes0.0000.0000.001
invertNodeSelection0.0010.0000.001
layout000
layoutSelectionInGrid000
layoutSelectionInGridInferAnchorm000
loadStyleFile000
noa000
noaNames0.0010.0000.000
redraw0.0000.0000.001
restoreLayout0.0000.0000.001
saveJPG000
saveLayout000
savePNG0.0000.0010.000
selectFirstNeighborsOfSelectedNodes0.0000.0010.000
selectNodes000
setBackgroundColor0.0000.0000.001
setDefaultEdgeColor0.0000.0000.001
setDefaultEdgeLineColor000
setDefaultEdgeLineStyle000
setDefaultEdgeSourceArrowColor000
setDefaultEdgeSourceArrowShape0.0010.0000.000
setDefaultEdgeTargetArrowColor000
setDefaultEdgeTargetArrowShape0.0010.0000.000
setDefaultEdgeWidth0.0010.0000.001
setDefaultNodeBorderColor0.0000.0000.001
setDefaultNodeBorderWidth000
setDefaultNodeColor000
setDefaultNodeFontColor0.0000.0010.000
setDefaultNodeFontSize000
setDefaultNodeHeight0.0000.0000.001
setDefaultNodeShape0.0000.0000.001
setDefaultNodeSize000
setDefaultNodeWidth000
setDefaultStyle000
setEdgeStyle0.0010.0000.000
setGraph0.0010.0000.000
setNodeAttributes0.0010.0000.001
setNodeBorderColor0.0000.0000.001
setNodeBorderWidth000
setNodeColor000
setNodeColorRule0.0000.0010.000
setNodeFontColor0.0000.0010.000
setNodeFontSize0.0000.0010.000
setNodeHeight000
setNodeLabelRule0.0000.0000.001
setNodeShape0.0000.0000.001
setNodeSize000
setNodeSizeRule000
setNodeWidth000
setPosition000
setZoom000
sfn0.0010.0000.001
showAll0.0010.0010.001
showEdges0.0000.0000.001
showNodes0.0000.0000.001
simpleDemoGraph0.0450.0010.047
vAlign000