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This page was generated on 2023-10-16 11:35:40 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1657/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.22.0  (landing page)
Paul Shannon
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/RCyjs
git_branch: RELEASE_3_17
git_last_commit: 4e01d9c
git_last_commit_date: 2023-04-25 10:39:11 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for RCyjs on nebbiolo1


To the developers/maintainers of the RCyjs package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RCyjs
Version: 2.22.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RCyjs_2.22.0.tar.gz
StartedAt: 2023-10-16 00:16:37 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 00:17:15 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 37.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RCyjs.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RCyjs_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RCyjs.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RCyjs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCyjs’ version ‘2.22.0’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ...
  ‘RCyjs.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/RCyjs.Rcheck/00check.log’
for details.



Installation output

RCyjs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RCyjs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 
  0.174   0.010   0.173 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0000.0000.001
addGraph0.0010.0000.000
addGraphFromFile0.0000.0000.001
clearSelection0.0000.0000.001
createTestGaph0.0060.0000.007
deleteGraph000
deleteSelectedNodes0.0010.0000.000
eda000
edaNames0.0000.0000.001
fit000
fitSelection000
getEdgeCount0.0000.0000.001
getJSON000
getLayoutStrategies000
getNodeCount0.0000.0010.000
getNodes000
getPosition000
getSelectedNodes0.0000.0010.000
getSupportedEdgeDecoratorShapes0.0000.0000.001
getSupportedNodeShapes000
getZoom0.0000.0010.000
graphNELtoJSON.string0.0000.0000.001
hAlign000
hideAllEdges0.0010.0000.000
hideEdges000
hideNodes0.0000.0000.001
hideSelectedNodes000
invertNodeSelection000
layout0.0000.0010.000
layoutSelectionInGrid0.0000.0010.001
layoutSelectionInGridInferAnchorm0.0000.0000.001
loadStyleFile000
noa000
noaNames000
redraw0.0000.0000.001
restoreLayout000
saveJPG0.0000.0010.000
saveLayout0.0000.0010.000
savePNG0.0000.0000.001
selectFirstNeighborsOfSelectedNodes0.0000.0000.001
selectNodes0.0010.0000.000
setBackgroundColor000
setDefaultEdgeColor0.0000.0000.001
setDefaultEdgeLineColor000
setDefaultEdgeLineStyle0.0010.0000.000
setDefaultEdgeSourceArrowColor0.0000.0000.001
setDefaultEdgeSourceArrowShape000
setDefaultEdgeTargetArrowColor0.0010.0000.000
setDefaultEdgeTargetArrowShape000
setDefaultEdgeWidth0.0000.0010.001
setDefaultNodeBorderColor000
setDefaultNodeBorderWidth000
setDefaultNodeColor0.0000.0010.000
setDefaultNodeFontColor0.0000.0000.001
setDefaultNodeFontSize000
setDefaultNodeHeight0.0010.0000.000
setDefaultNodeShape0.0000.0000.001
setDefaultNodeSize000
setDefaultNodeWidth0.0010.0000.000
setDefaultStyle000
setEdgeStyle000
setGraph0.0000.0000.001
setNodeAttributes0.0010.0000.000
setNodeBorderColor000
setNodeBorderWidth0.0000.0000.001
setNodeColor000
setNodeColorRule0.0010.0000.000
setNodeFontColor000
setNodeFontSize0.0000.0000.001
setNodeHeight000
setNodeLabelRule0.0010.0000.000
setNodeShape000
setNodeSize0.0000.0000.001
setNodeSizeRule0.0010.0000.000
setNodeWidth0.0010.0000.000
setPosition000
setZoom0.0000.0000.001
sfn000
showAll0.0010.0000.000
showEdges000
showNodes0.0000.0000.001
simpleDemoGraph0.0470.0000.047
vAlign0.0000.0010.001