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This page was generated on 2024-05-22 11:35:09 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 3444
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 1707/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.26.1  (landing page)
Paul Shannon
Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 2024)
git_url: https://git.bioconductor.org/packages/RCyjs
git_branch: RELEASE_3_19
git_last_commit: d14903d
git_last_commit_date: 2024-04-30 15:42:03 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / 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: 2.26.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RCyjs_2.26.1.tar.gz
StartedAt: 2024-05-22 02:08:47 -0400 (Wed, 22 May 2024)
EndedAt: 2024-05-22 02:09:26 -0400 (Wed, 22 May 2024)
EllapsedTime: 39.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RCyjs.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RCyjs_2.26.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RCyjs.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘RCyjs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCyjs’ version ‘2.26.1’
* 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether 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 Rd file 'hideNodes.Rd'
  ‘nodeIDs’

Undocumented arguments in Rd file 'readAndStandardizeJSONNetworkFile.Rd'
  ‘filename’
Documented arguments not in \usage in Rd file 'readAndStandardizeJSONNetworkFile.Rd':
  ‘file’

Undocumented arguments in Rd file 'readAndStandardizeJSONStyleFile.Rd'
  ‘filename’
Documented arguments not in \usage in Rd file 'readAndStandardizeJSONStyleFile.Rd':
  ‘file’

Undocumented arguments in Rd file 'showNodes.Rd'
  ‘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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/RCyjs.Rcheck/00check.log’
for details.


Installation output

RCyjs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RCyjs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.176   0.020   0.183 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0000.0000.001
addGraph000
addGraphFromFile0.0010.0000.000
clearSelection0.0000.0000.001
createTestGaph0.0060.0000.007
deleteGraph0.0000.0000.001
deleteSelectedNodes0.0000.0000.001
eda000
edaNames000
fit0.0000.0000.001
fitSelection000
getEdgeCount000
getJSON0.0000.0010.001
getLayoutStrategies000
getNodeCount000
getNodes0.0000.0010.001
getPosition000
getSelectedNodes000
getSupportedEdgeDecoratorShapes0.0000.0000.001
getSupportedNodeShapes0.0000.0010.000
getZoom000
graphNELtoJSON.string000
hAlign0.0000.0010.001
hideAllEdges000
hideEdges000
hideNodes0.0000.0000.001
hideSelectedNodes0.0000.0000.001
invertNodeSelection000
layout000
layoutSelectionInGrid0.0010.0000.000
layoutSelectionInGridInferAnchorm0.0010.0010.000
loadStyleFile0.0000.0000.001
noa000
noaNames000
redraw0.0000.0000.001
restoreLayout0.0000.0010.001
saveJPG0.0000.0010.000
saveLayout000
savePNG000
selectFirstNeighborsOfSelectedNodes0.0000.0000.001
selectNodes0.0000.0010.000
setBackgroundColor000
setDefaultEdgeColor000
setDefaultEdgeLineColor0.0000.0000.001
setDefaultEdgeLineStyle000
setDefaultEdgeSourceArrowColor0.0010.0000.000
setDefaultEdgeSourceArrowShape0.0000.0000.001
setDefaultEdgeTargetArrowColor000
setDefaultEdgeTargetArrowShape0.0010.0000.000
setDefaultEdgeWidth000
setDefaultNodeBorderColor0.0000.0000.001
setDefaultNodeBorderWidth000
setDefaultNodeColor0.0010.0000.000
setDefaultNodeFontColor000
setDefaultNodeFontSize0.0000.0000.001
setDefaultNodeHeight000
setDefaultNodeShape0.0010.0000.000
setDefaultNodeSize0.0000.0000.001
setDefaultNodeWidth000
setDefaultStyle000
setEdgeStyle000
setGraph000
setNodeAttributes0.0000.0010.001
setNodeBorderColor000
setNodeBorderWidth0.0010.0000.000
setNodeColor000
setNodeColorRule0.0000.0000.001
setNodeFontColor000
setNodeFontSize0.0010.0010.000
setNodeHeight000
setNodeLabelRule0.0000.0000.001
setNodeShape000
setNodeSize0.0010.0000.000
setNodeSizeRule000
setNodeWidth0.0000.0000.001
setPosition0.0000.0010.000
setZoom000
sfn000
showAll0.0000.0000.001
showEdges0.0000.0010.001
showNodes000
simpleDemoGraph0.0400.0030.042
vAlign000