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This page was generated on 2021-06-23 15:06:10 -0400 (Wed, 23 Jun 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: 2021-06-22 04:50:12 -0400 (Tue, 22 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: /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: 2021-06-22 22:44:19 -0400 (Tue, 22 Jun 2021)
EndedAt: 2021-06-22 22:45:12 -0400 (Tue, 22 Jun 2021)
EllapsedTime: 53.5 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 4.1.0 (2021-05-18)
* 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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 
  0.262   0.066   0.305 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0010.0010.002
addGraph0.0000.0000.001
addGraphFromFile0.0010.0000.001
clearSelection0.0000.0000.001
createTestGaph0.0080.0000.009
deleteGraph0.0000.0010.001
deleteSelectedNodes000
eda0.0000.0010.000
edaNames0.0010.0000.000
fit0.0000.0010.001
fitSelection0.0000.0000.001
getEdgeCount000
getJSON0.0000.0000.001
getLayoutStrategies0.0010.0000.000
getNodeCount0.0000.0010.001
getNodes000
getPosition000
getSelectedNodes0.0010.0000.001
getSupportedEdgeDecoratorShapes0.0010.0010.001
getSupportedNodeShapes0.0000.0010.000
getZoom0.0010.0000.000
graphNELtoJSON.string000
hAlign0.0000.0010.001
hideAllEdges0.0010.0000.001
hideEdges0.0000.0000.001
hideNodes0.0010.0000.001
hideSelectedNodes0.0000.0000.001
invertNodeSelection000
layout0.0010.0000.001
layoutSelectionInGrid0.0010.0000.002
layoutSelectionInGridInferAnchorm0.0000.0010.001
loadStyleFile0.0010.0010.001
noa0.0010.0000.000
noaNames000
redraw000
restoreLayout0.0000.0000.001
saveJPG0.0010.0000.002
saveLayout0.0000.0000.001
savePNG0.0010.0010.001
selectFirstNeighborsOfSelectedNodes0.0000.0000.001
selectNodes0.0000.0000.001
setBackgroundColor000
setDefaultEdgeColor0.0010.0000.001
setDefaultEdgeLineColor0.0000.0000.001
setDefaultEdgeLineStyle0.0010.0000.000
setDefaultEdgeSourceArrowColor0.0010.0010.000
setDefaultEdgeSourceArrowShape000
setDefaultEdgeTargetArrowColor000
setDefaultEdgeTargetArrowShape000
setDefaultEdgeWidth0.0010.0000.001
setDefaultNodeBorderColor0.0000.0010.001
setDefaultNodeBorderWidth000
setDefaultNodeColor0.0000.0010.001
setDefaultNodeFontColor0.0000.0010.001
setDefaultNodeFontSize0.0010.0000.001
setDefaultNodeHeight0.0010.0000.001
setDefaultNodeShape0.0010.0000.000
setDefaultNodeSize0.0010.0000.001
setDefaultNodeWidth0.0010.0000.001
setDefaultStyle0.0000.0010.001
setEdgeStyle0.0010.0010.001
setGraph0.0000.0010.001
setNodeAttributes0.0010.0010.001
setNodeBorderColor0.0000.0010.001
setNodeBorderWidth000
setNodeColor0.0000.0000.001
setNodeColorRule0.0010.0000.001
setNodeFontColor0.0000.0000.001
setNodeFontSize0.0010.0000.001
setNodeHeight0.0000.0000.001
setNodeLabelRule0.0000.0010.001
setNodeShape0.0010.0010.001
setNodeSize0.0010.0010.000
setNodeSizeRule0.0000.0000.001
setNodeWidth0.0010.0000.001
setPosition0.0010.0000.001
setZoom000
sfn0.0010.0000.001
showAll0.0000.0010.001
showEdges0.0010.0010.001
showNodes0.0000.0010.001
simpleDemoGraph0.0930.0010.094
vAlign0.0010.0000.000