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This page was generated on 2022-06-24 11:07:03 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

CHECK results for RCyjs on palomino4


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? 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 1577/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.19.0  (landing page)
Paul Shannon
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/RCyjs
git_branch: master
git_last_commit: 64ee431
git_last_commit_date: 2022-04-26 11:25:00 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RCyjs
Version: 2.19.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCyjs.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings RCyjs_2.19.0.tar.gz
StartedAt: 2022-06-24 04:53:31 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:54:23 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 52.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RCyjs.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCyjs.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings RCyjs_2.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/RCyjs.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 '2.19.0'
* 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 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
See
  'F:/biocbuild/bbs-3.16-bioc/meat/RCyjs.Rcheck/00check.log'
for details.



Installation output

RCyjs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/RCyjs_2.19.0.tar.gz && rm -rf RCyjs.buildbin-libdir && mkdir RCyjs.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCyjs.buildbin-libdir RCyjs_2.19.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL RCyjs_2.19.0.zip && rm RCyjs_2.19.0.tar.gz RCyjs_2.19.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1  892k    1 13437    0     0   360k      0  0:00:02 --:--:--  0:00:02  364k
100  892k  100  892k    0     0  3418k      0 --:--:-- --:--:-- --:--:-- 3418k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'RCyjs' as RCyjs_2.19.0.zip
* DONE (RCyjs)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'RCyjs' successfully unpacked and MD5 sums checked

Tests output

RCyjs.Rcheck/tests/runTests.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   0.17    0.06    0.20 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class000
addGraph000
addGraphFromFile000
clearSelection000
createTestGaph0.020.000.02
deleteGraph000
deleteSelectedNodes000
eda000
edaNames000
fit000
fitSelection000
getEdgeCount000
getJSON000
getLayoutStrategies000
getNodeCount000
getNodes000
getPosition000
getSelectedNodes000
getSupportedEdgeDecoratorShapes000
getSupportedNodeShapes000
getZoom000
graphNELtoJSON.string000
hAlign000
hideAllEdges000
hideEdges000
hideNodes000
hideSelectedNodes000
invertNodeSelection000
layout000
layoutSelectionInGrid000
layoutSelectionInGridInferAnchorm000
loadStyleFile000
noa000
noaNames000
redraw000
restoreLayout000
saveJPG000
saveLayout000
savePNG000
selectFirstNeighborsOfSelectedNodes000
selectNodes000
setBackgroundColor000
setDefaultEdgeColor000
setDefaultEdgeLineColor000
setDefaultEdgeLineStyle000
setDefaultEdgeSourceArrowColor000
setDefaultEdgeSourceArrowShape000
setDefaultEdgeTargetArrowColor000
setDefaultEdgeTargetArrowShape000
setDefaultEdgeWidth000
setDefaultNodeBorderColor000
setDefaultNodeBorderWidth000
setDefaultNodeColor000
setDefaultNodeFontColor000
setDefaultNodeFontSize000
setDefaultNodeHeight000
setDefaultNodeShape000
setDefaultNodeSize0.020.000.01
setDefaultNodeWidth000
setDefaultStyle000
setEdgeStyle000
setGraph000
setNodeAttributes000
setNodeBorderColor000
setNodeBorderWidth000
setNodeColor000
setNodeColorRule000
setNodeFontColor000
setNodeFontSize000
setNodeHeight000
setNodeLabelRule000
setNodeShape000
setNodeSize000
setNodeSizeRule000
setNodeWidth000
setPosition000
setZoom000
sfn000
showAll000
showEdges000
showNodes000
simpleDemoGraph0.030.000.03
vAlign000