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This page was generated on 2025-10-06 12:05 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1860/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rWikiPathways 1.29.1  (landing page)
Egon Willighagen
Snapshot Date: 2025-10-05 13:45 -0400 (Sun, 05 Oct 2025)
git_url: https://git.bioconductor.org/packages/rWikiPathways
git_branch: devel
git_last_commit: ab313f2
git_last_commit_date: 2025-09-07 07:23:12 -0400 (Sun, 07 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for rWikiPathways on lconway

To the developers/maintainers of the rWikiPathways package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rWikiPathways.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: rWikiPathways
Version: 1.29.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rWikiPathways_1.29.1.tar.gz
StartedAt: 2025-10-06 00:17:49 -0400 (Mon, 06 Oct 2025)
EndedAt: 2025-10-06 00:20:16 -0400 (Mon, 06 Oct 2025)
EllapsedTime: 146.8 seconds
RetCode: 0
Status:   OK  
CheckDir: rWikiPathways.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rWikiPathways_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/rWikiPathways.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rWikiPathways/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rWikiPathways’ version ‘1.29.1’
* package encoding: UTF-8
* 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 ... NOTE
Found the following non-portable file path:
  rWikiPathways/docs/articles/rWikiPathways-and-BridgeDbR_files/accessible-code-block-0.0.1/empty-anchor.js

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rWikiPathways’ 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 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 ... NOTE
findPathwaysByLiterature: no visible binding for global variable ‘refs’
findPathwaysByLiterature: no visible binding for global variable
  ‘citations’
findPathwaysByOrcid: no visible binding for global variable ‘orcids’
findPathwaysByText: no visible binding for global variable ‘citedIn’
getOntologyTerms: no visible binding for global variable ‘terms’
getPathwaysByCommunity: no visible binding for global variable
  ‘pathways’
getPathwaysByCommunity: no visible binding for global variable
  ‘community-tag’
getPathwaysByOntologyTerm: no visible binding for global variable
  ‘pathways’
getPathwaysByParentOntologyTerm: no visible binding for global variable
  ‘terms’
getPathwaysByParentOntologyTerm: no visible binding for global variable
  ‘terms_parent’
getRecentChanges: no visible binding for global variable ‘revision’
getRecentChanges: no visible binding for global variable ‘revision_ymd’
getRecentChanges: no visible binding for global variable ‘authors’
getRecentChanges: no visible binding for global variable ‘description’
getRecentChanges: no visible binding for global variable ‘citedIn’
listCommunities: no visible binding for global variable ‘pathways’
listPathways: no visible binding for global variable ‘species’
readPathwayGMT: no visible binding for global variable ‘pathway’
Undefined global functions or variables:
  authors citations citedIn community-tag description orcids pathway
  pathways refs revision revision_ymd species terms terms_parent
Consider adding
  importFrom("stats", "terms")
to your NAMESPACE file.
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
findPathwaysByLiterature     9.192  0.140   9.975
findPathwayUrlsByLiterature  7.353  0.116   8.439
findPathwayIdsByLiterature   7.253  0.124   8.029
findPathwayNamesByLiterature 7.004  0.120   7.585
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.


Installation output

rWikiPathways.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘rWikiPathways’ ...
** this is package ‘rWikiPathways’ version ‘1.29.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (rWikiPathways)

Tests output

rWikiPathways.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> library(testthat)
> library(rWikiPathways)
> 
> test_check("rWikiPathways")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 26 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 23.856   0.683  28.135 

Example timings

rWikiPathways.Rcheck/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive0.0000.0010.000
findPathwayIDsByOrcid0.3870.0210.849
findPathwayIdsByLiterature7.2530.1248.029
findPathwayIdsByText2.4740.0292.765
findPathwayIdsByXref1.3670.0461.842
findPathwayNamesByLiterature7.0040.1207.585
findPathwayNamesByOrcid0.3840.0120.537
findPathwayNamesByText2.3970.0272.573
findPathwayNamesByXref1.2740.0371.453
findPathwayUrlsByLiterature7.3530.1168.439
findPathwayUrlsByOrcid0.4260.0120.598
findPathwayUrlsByText2.3350.0252.524
findPathwayUrlsByXref1.0530.0251.322
findPathwaysByLiterature9.1920.1409.975
findPathwaysByOrcid0.4160.0180.589
findPathwaysByText2.8430.0453.297
findPathwaysByXref1.1740.0301.630
getCounts0.0160.0020.121
getCurationStatus0.0150.0010.122
getOntologyTermIds1.2750.0231.604
getOntologyTermNames1.1600.0151.352
getOntologyTerms1.2470.0161.402
getPathway0.0450.0060.154
getPathwayHistory0.0000.0010.000
getPathwayIdsByCommunity0.2110.0080.377
getPathwayIdsByOntologyTerm0.1610.0060.325
getPathwayIdsByParentOntologyTerm1.4000.0191.558
getPathwayInfo0.2910.0120.543
getPathwayNamesByCommunity0.1870.0090.314
getPathwayUrlsByCommunity0.1590.0070.284
getPathwaysByCommunity0.2000.0090.331
getPathwaysByOntologyTerm0.1390.0060.252
getPathwaysByParentOntologyTerm1.1450.0571.345
getRecentChanges0.6080.0970.836
getRecentChangesIds0.3060.0270.454
getRecentChangesNames0.3250.0390.519
getXrefList0.2910.0450.451
listCommunities0.1950.0080.329
listOrganisms0.0130.0020.113
listPathwayIds0.1790.0080.360
listPathwayNames0.3750.0130.515
listPathwayUrls0.1530.0080.296
listPathways0.1730.0130.318
readGMT0.0000.0010.000
readGMTnames000
readPathwayGMT000
writeGMT000