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This page was generated on 2025-10-15 12:07 -0400 (Wed, 15 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4866
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4653
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4598
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 1865/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rWikiPathways 1.29.1  (landing page)
Egon Willighagen
Snapshot Date: 2025-10-14 13:45 -0400 (Tue, 14 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 12.7.6 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: rWikiPathways
Version: 1.29.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rWikiPathways_1.29.1.tar.gz
StartedAt: 2025-10-14 12:19:23 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 12:24:22 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 298.3 seconds
RetCode: 0
Status:   OK  
CheckDir: rWikiPathways.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rWikiPathways_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/rWikiPathways.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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     11.509  0.114  25.246
findPathwayIdsByLiterature    8.460  0.300  16.133
findPathwayUrlsByLiterature   8.210  0.044  17.091
findPathwayNamesByLiterature  8.090  0.120  15.280
findPathwaysByText            3.501  0.045   7.039
findPathwayIdsByXref          1.230  0.120  11.154
findPathwayNamesByXref        1.270  0.059   8.370
findPathwaysByXref            1.160  0.054  11.499
findPathwayUrlsByXref         1.161  0.036  10.540
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.


Installation output

rWikiPathways.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL rWikiPathways
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 28.390   0.666  89.455 

Example timings

rWikiPathways.Rcheck/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive000
findPathwayIDsByOrcid0.4140.0071.596
findPathwayIdsByLiterature 8.460 0.30016.133
findPathwayIdsByText3.1580.0404.462
findPathwayIdsByXref 1.230 0.12011.154
findPathwayNamesByLiterature 8.09 0.1215.28
findPathwayNamesByOrcid0.4000.0150.875
findPathwayNamesByText3.1170.0164.866
findPathwayNamesByXref1.2700.0598.370
findPathwayUrlsByLiterature 8.210 0.04417.091
findPathwayUrlsByOrcid0.3970.0000.855
findPathwayUrlsByText3.0510.0284.189
findPathwayUrlsByXref 1.161 0.03610.540
findPathwaysByLiterature11.509 0.11425.246
findPathwaysByOrcid0.4170.0040.879
findPathwaysByText3.5010.0457.039
findPathwaysByXref 1.160 0.05411.499
getCounts0.0230.0000.742
getCurationStatus0.0180.0040.726
getOntologyTermIds1.4260.0042.166
getOntologyTermNames1.6120.0112.351
getOntologyTerms1.3010.0112.514
getPathway0.0520.0040.353
getPathwayHistory000
getPathwayIdsByCommunity0.1990.0040.932
getPathwayIdsByOntologyTerm0.1540.0041.093
getPathwayIdsByParentOntologyTerm1.3650.0161.849
getPathwayInfo0.4030.0151.141
getPathwayNamesByCommunity0.1970.0040.655
getPathwayUrlsByCommunity0.1850.0110.650
getPathwaysByCommunity0.2030.0000.655
getPathwaysByOntologyTerm0.1340.0110.597
getPathwaysByParentOntologyTerm1.4090.0041.876
getRecentChanges0.6260.0331.356
getRecentChangesIds0.3310.0040.781
getRecentChangesNames0.3370.0081.753
getXrefList0.3680.0160.649
listCommunities0.2580.0000.726
listOrganisms0.0180.0000.721
listPathwayIds0.2150.0000.949
listPathwayNames0.2210.0000.678
listPathwayUrls0.2170.0000.664
listPathways0.2190.0280.710
readGMT0.0000.0000.001
readGMTnames000
readPathwayGMT000
writeGMT000