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This page was generated on 2025-09-01 12:04 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1845/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rWikiPathways 1.29.0  (landing page)
Egon Willighagen
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025)
git_url: https://git.bioconductor.org/packages/rWikiPathways
git_branch: devel
git_last_commit: 7f79176
git_last_commit_date: 2025-04-15 11:20:27 -0400 (Tue, 15 Apr 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 nebbiolo2

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: 1.29.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings rWikiPathways_1.29.0.tar.gz
StartedAt: 2025-09-01 02:36:04 -0400 (Mon, 01 Sep 2025)
EndedAt: 2025-09-01 02:38:08 -0400 (Mon, 01 Sep 2025)
EllapsedTime: 124.1 seconds
RetCode: 0
Status:   OK  
CheckDir: rWikiPathways.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings rWikiPathways_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/rWikiPathways.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rWikiPathways/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rWikiPathways’ version ‘1.29.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 loading without being on the library search path ... 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     8.343  0.008   8.643
findPathwayIdsByLiterature   6.224  0.115   6.776
findPathwayNamesByLiterature 6.093  0.045   6.370
findPathwayUrlsByLiterature  6.100  0.022   6.386
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.


Installation output

rWikiPathways.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL rWikiPathways
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘rWikiPathways’ ...
** this is package ‘rWikiPathways’ version ‘1.29.0’
** 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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.

> 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 
 22.050   0.753  24.306 

Example timings

rWikiPathways.Rcheck/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive000
findPathwayIDsByOrcid0.3710.0130.612
findPathwayIdsByLiterature6.2240.1156.776
findPathwayIdsByText2.2000.0242.311
findPathwayIdsByXref1.2140.0431.330
findPathwayNamesByLiterature6.0930.0456.370
findPathwayNamesByOrcid0.3560.0030.541
findPathwayNamesByText2.1920.0052.262
findPathwayNamesByXref1.1510.0221.250
findPathwayUrlsByLiterature6.1000.0226.386
findPathwayUrlsByOrcid0.3480.0010.427
findPathwayUrlsByText2.1880.0042.264
findPathwayUrlsByXref1.0870.0141.169
findPathwaysByLiterature8.3430.0088.643
findPathwaysByOrcid0.3700.0020.459
findPathwaysByText2.5690.0062.718
findPathwaysByXref1.1310.0201.230
getCounts0.0450.0010.098
getCurationStatus0.0460.0000.097
getOntologyTermIds1.2130.0071.290
getOntologyTermNames0.9390.0031.007
getOntologyTerms1.0180.0051.197
getPathway0.0770.0070.160
getPathwayHistory000
getPathwayIdsByCommunity0.2090.0000.307
getPathwayIdsByOntologyTerm0.1880.0000.268
getPathwayIdsByParentOntologyTerm1.3220.0031.388
getPathwayInfo0.2710.0020.458
getPathwayNamesByCommunity0.1960.0000.254
getPathwayUrlsByCommunity0.2000.0000.262
getPathwaysByCommunity0.2120.0020.311
getPathwaysByOntologyTerm0.1680.0020.235
getPathwaysByParentOntologyTerm0.9850.0101.062
getRecentChanges0.5930.0220.682
getRecentChangesIds0.2690.0050.444
getRecentChangesNames0.2870.0050.349
getXrefList0.2580.0260.362
listCommunities0.1850.0000.267
listOrganisms0.0420.0020.107
listPathwayIds0.1950.0010.284
listPathwayNames0.1800.0030.262
listPathwayUrls0.1850.0030.269
listPathways0.1950.0030.282
readGMT000
readGMTnames000
readPathwayGMT000
writeGMT000