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This page was generated on 2024-03-04 11:37:44 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1687/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.24.0  (landing page)
Paul Shannon
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/RCyjs
git_branch: RELEASE_3_18
git_last_commit: 51a82aa
git_last_commit_date: 2023-10-24 10:42:58 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for RCyjs on lconway


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: 2.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCyjs_2.24.0.tar.gz
StartedAt: 2024-03-03 22:51:13 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 22:52:09 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 56.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RCyjs.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCyjs_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/RCyjs.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCyjs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCyjs’ version ‘2.24.0’
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/RCyjs.Rcheck/00check.log’
for details.



Installation output

RCyjs.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
  0.209   0.075   0.277 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0010.0010.001
addGraph0.0010.0000.000
addGraphFromFile0.0010.0010.001
clearSelection0.0010.0000.002
createTestGaph0.0090.0000.009
deleteGraph000
deleteSelectedNodes0.0010.0000.002
eda0.0010.0000.001
edaNames0.0010.0010.001
fit000
fitSelection000
getEdgeCount000
getJSON0.0000.0000.001
getLayoutStrategies0.0000.0000.001
getNodeCount0.0000.0000.001
getNodes000
getPosition0.0000.0000.001
getSelectedNodes000
getSupportedEdgeDecoratorShapes0.0000.0000.001
getSupportedNodeShapes000
getZoom0.0000.0000.001
graphNELtoJSON.string0.0000.0000.001
hAlign0.0010.0010.001
hideAllEdges0.0010.0010.000
hideEdges0.0010.0010.001
hideNodes0.0010.0010.001
hideSelectedNodes0.0010.0010.001
invertNodeSelection0.0010.0010.001
layout0.0010.0010.001
layoutSelectionInGrid0.0010.0010.001
layoutSelectionInGridInferAnchorm0.0010.0010.001
loadStyleFile0.0000.0010.001
noa0.0010.0000.001
noaNames000
redraw0.0000.0000.001
restoreLayout0.0000.0000.001
saveJPG0.0000.0000.001
saveLayout0.0000.0000.001
savePNG0.0000.0000.001
selectFirstNeighborsOfSelectedNodes0.0000.0000.001
selectNodes000
setBackgroundColor0.0000.0000.001
setDefaultEdgeColor000
setDefaultEdgeLineColor0.0010.0000.000
setDefaultEdgeLineStyle0.0010.0000.000
setDefaultEdgeSourceArrowColor0.0000.0000.001
setDefaultEdgeSourceArrowShape0.0000.0010.001
setDefaultEdgeTargetArrowColor0.0000.0010.000
setDefaultEdgeTargetArrowShape0.0000.0010.000
setDefaultEdgeWidth0.0010.0010.001
setDefaultNodeBorderColor0.0000.0000.001
setDefaultNodeBorderWidth000
setDefaultNodeColor0.0000.0000.001
setDefaultNodeFontColor0.0010.0000.000
setDefaultNodeFontSize0.0000.0000.001
setDefaultNodeHeight0.0000.0000.001
setDefaultNodeShape0.0000.0000.001
setDefaultNodeSize0.0000.0000.001
setDefaultNodeWidth0.0010.0000.000
setDefaultStyle0.0000.0010.001
setEdgeStyle0.0000.0010.001
setGraph000
setNodeAttributes0.0010.0000.001
setNodeBorderColor000
setNodeBorderWidth0.0000.0000.001
setNodeColor0.0000.0000.001
setNodeColorRule0.0000.0000.001
setNodeFontColor0.0010.0000.000
setNodeFontSize000
setNodeHeight0.0000.0000.001
setNodeLabelRule0.0010.0000.001
setNodeShape000
setNodeSize0.0000.0000.001
setNodeSizeRule0.0000.0010.002
setNodeWidth0.0010.0010.001
setPosition0.0010.0010.001
setZoom0.0010.0010.001
sfn0.0010.0000.001
showAll0.0010.0000.001
showEdges0.0010.0000.004
showNodes0.0010.0000.002
simpleDemoGraph0.0670.0010.068
vAlign0.0010.0000.001