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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbChebi_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.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 ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.14.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 ... 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘biodbChebi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ChebiConn
> ### Title: ChEBI connector class.
> ### Aliases: ChebiConn
> 
> ### ** Examples
> 
> # Create an instance with default settings:
> mybiodb <- biodb::newInst()
INFO  [21:25:51.446] Loading definitions from package biodb version 1.16.0.
INFO  [21:25:51.859] Loading definitions from package biodbChebi version 1.14.0.
> 
> # Create a connector
> conn <- mybiodb$getFactory()$createConn('chebi')
> 
> # Get an entry
> e <- conn$getEntry('15440')
> 
> # Convert an InChI KEY to a ChEBI identifier
> conn$convInchiToChebi('YYGNTYWPHWGJRM-AAJYLUCBSA-N')
INFO  [21:25:53.588] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO  [21:25:54.454] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO  [21:25:55.306] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO  [21:25:56.073] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO  [21:25:56.926] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO  [21:25:57.782] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO  [21:25:58.699] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO  [21:25:59.580] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO  [21:26:00.353] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO  [21:26:01.128] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
Error in if (file == "" || length(file) == 0) stop("empty or no content specified") : 
  missing value where TRUE/FALSE needed
Calls: <Anonymous> -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
   3.   └─conn$annotateMzValues(...)
   4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
   5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
   6.         └─private$searchByMass(...)
   7.           └─self$wsGetLiteEntity(...)
   8.             └─XML::xmlInternalTreeParse(results, asText = TRUE)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 179 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck/00check.log’
for details.