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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings rWikiPathways_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-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 ‘1.28.0’
* 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     8.467  0.014   8.779
findPathwayIdsByLiterature   6.453  0.297   7.189
findPathwayNamesByLiterature 6.203  0.051   6.468
findPathwayUrlsByLiterature  6.199  0.017   6.428
* 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-3.21-bioc/meat/rWikiPathways.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL rWikiPathways
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘rWikiPathways’ ...
** this is package ‘rWikiPathways’ version ‘1.28.0’
** 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)

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 
 22.026   0.756  24.365