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This page was generated on 2021-07-23 15:05:48 -0400 (Fri, 23 Jul 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: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 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: 2021-07-22 11:12:25 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 11:12:59 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 33.7 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 
  0.164   0.048   0.197 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0010.0000.001
addGraph0.0010.0000.000
addGraphFromFile0.0010.0000.001
clearSelection0.0000.0000.001
createTestGaph0.0060.0000.006
deleteGraph000
deleteSelectedNodes0.0010.0000.001
eda0.0010.0000.001
edaNames000
fit000
fitSelection000
getEdgeCount0.0010.0000.001
getJSON000
getLayoutStrategies000
getNodeCount000
getNodes0.0000.0000.001
getPosition0.0000.0000.001
getSelectedNodes0.0000.0010.000
getSupportedEdgeDecoratorShapes000
getSupportedNodeShapes000
getZoom0.0000.0000.001
graphNELtoJSON.string0.0000.0000.001
hAlign0.0000.0010.000
hideAllEdges000
hideEdges000
hideNodes000
hideSelectedNodes000
invertNodeSelection0.0010.0000.001
layout0.0010.0000.001
layoutSelectionInGrid0.0010.0000.001
layoutSelectionInGridInferAnchorm0.0010.0000.001
loadStyleFile000
noa000
noaNames000
redraw0.0010.0000.001
restoreLayout0.0010.0000.001
saveJPG0.0000.0000.001
saveLayout000
savePNG000
selectFirstNeighborsOfSelectedNodes000
selectNodes000
setBackgroundColor0.0010.0000.001
setDefaultEdgeColor0.0000.0000.001
setDefaultEdgeLineColor000
setDefaultEdgeLineStyle000
setDefaultEdgeSourceArrowColor000
setDefaultEdgeSourceArrowShape000
setDefaultEdgeTargetArrowColor0.0000.0000.001
setDefaultEdgeTargetArrowShape0.0000.0010.001
setDefaultEdgeWidth0.0000.0010.000
setDefaultNodeBorderColor000
setDefaultNodeBorderWidth000
setDefaultNodeColor0.0000.0000.001
setDefaultNodeFontColor0.0000.0000.001
setDefaultNodeFontSize0.0000.0010.000
setDefaultNodeHeight0.0000.0010.000
setDefaultNodeShape000
setDefaultNodeSize000
setDefaultNodeWidth0.0000.0000.001
setDefaultStyle0.0000.0010.001
setEdgeStyle0.0000.0010.000
setGraph000
setNodeAttributes000
setNodeBorderColor000
setNodeBorderWidth0.0010.0000.001
setNodeColor0.0000.0000.001
setNodeColorRule000
setNodeFontColor000
setNodeFontSize000
setNodeHeight000
setNodeLabelRule0.0010.0000.001
setNodeShape0.0000.0000.001
setNodeSize000
setNodeSizeRule0.0000.0010.000
setNodeWidth000
setPosition000
setZoom000
sfn0.0000.0000.001
showAll0.0000.0010.001
showEdges0.0000.0010.000
showNodes0.0000.0010.000
simpleDemoGraph0.0460.0000.046
vAlign0.0000.0000.001