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This page was generated on 2021-09-27 15:07:09 -0400 (Mon, 27 Sep 2021).

CHECK results for RCyjs on machv2

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: 2021-09-26 04:50:10 -0400 (Sun, 26 Sep 2021)
git_url: https://git.bioconductor.org/packages/RCyjs
git_branch: RELEASE_3_13
git_last_commit: d93cc23
git_last_commit_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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCyjs_2.14.0.tar.gz
StartedAt: 2021-09-26 22:52:34 -0400 (Sun, 26 Sep 2021)
EndedAt: 2021-09-26 22:53:27 -0400 (Sun, 26 Sep 2021)
EllapsedTime: 53.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RCyjs.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCyjs_2.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/RCyjs.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
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 ‘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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/RCyjs.Rcheck/00check.log’
for details.



Installation output

RCyjs.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RCyjs
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.249   0.060   0.287 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0010.0000.001
addGraph0.0000.0000.001
addGraphFromFile0.0000.0010.000
clearSelection0.0000.0000.001
createTestGaph0.0070.0000.007
deleteGraph0.0000.0000.001
deleteSelectedNodes000
eda0.0010.0000.000
edaNames0.0000.0000.001
fit0.0000.0000.001
fitSelection0.0010.0000.000
getEdgeCount000
getJSON000
getLayoutStrategies0.0000.0000.001
getNodeCount0.0000.0000.001
getNodes000
getPosition0.0000.0010.000
getSelectedNodes0.0010.0000.000
getSupportedEdgeDecoratorShapes0.0000.0000.001
getSupportedNodeShapes0.0000.0000.001
getZoom000
graphNELtoJSON.string000
hAlign0.0000.0010.000
hideAllEdges0.0000.0000.001
hideEdges0.0010.0000.000
hideNodes0.0010.0000.001
hideSelectedNodes0.0010.0000.001
invertNodeSelection000
layout0.0000.0000.001
layoutSelectionInGrid0.0000.0010.000
layoutSelectionInGridInferAnchorm0.0000.0000.001
loadStyleFile0.0000.0010.001
noa0.0000.0000.001
noaNames0.0000.0000.001
redraw0.0000.0000.001
restoreLayout0.0010.0000.001
saveJPG0.0000.0000.001
saveLayout0.0000.0010.000
savePNG0.0010.0000.001
selectFirstNeighborsOfSelectedNodes0.0010.0010.001
selectNodes0.0010.0000.000
setBackgroundColor0.0000.0000.001
setDefaultEdgeColor0.0000.0000.001
setDefaultEdgeLineColor000
setDefaultEdgeLineStyle0.0010.0000.000
setDefaultEdgeSourceArrowColor0.0000.0000.001
setDefaultEdgeSourceArrowShape0.0000.0000.001
setDefaultEdgeTargetArrowColor000
setDefaultEdgeTargetArrowShape0.0010.0000.001
setDefaultEdgeWidth000
setDefaultNodeBorderColor0.0000.0010.000
setDefaultNodeBorderWidth000
setDefaultNodeColor0.0010.0010.001
setDefaultNodeFontColor000
setDefaultNodeFontSize0.0000.0010.000
setDefaultNodeHeight0.0000.0000.001
setDefaultNodeShape0.0010.0000.000
setDefaultNodeSize0.0000.0000.001
setDefaultNodeWidth0.0000.0000.001
setDefaultStyle000
setEdgeStyle0.0000.0000.001
setGraph0.0010.0010.001
setNodeAttributes000
setNodeBorderColor0.0000.0010.000
setNodeBorderWidth0.0000.0000.001
setNodeColor0.0010.0010.000
setNodeColorRule000
setNodeFontColor0.0000.0000.001
setNodeFontSize000
setNodeHeight000
setNodeLabelRule0.0010.0000.001
setNodeShape0.0000.0000.001
setNodeSize000
setNodeSizeRule000
setNodeWidth0.0010.0000.001
setPosition0.0010.0000.000
setZoom000
sfn0.0000.0000.001
showAll0.0000.0010.000
showEdges0.0000.0000.001
showNodes0.0010.0010.001
simpleDemoGraph0.0850.0010.086
vAlign0.0000.0010.000