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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MsBackendMetaboLights_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MsBackendMetaboLights.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendMetaboLights/DESCRIPTION’ ... OK
* this is package ‘MsBackendMetaboLights’ version ‘1.1.0’
* 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 ‘MsBackendMetaboLights’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MsBackendMetaboLights.Rd: MsBackendMzR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ‘MsBackendMetaboLights-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MetaboLights-utils
> ### Title: Utility functions for the MetaboLights repository
> ### Aliases: MetaboLights-utils mtbls_ftp_path mtbls_list_files
> ###   mtbls_sync_data_files mtbls_cached_data_files
> 
> ### ** Examples
> 
> 
> ## Get the FTP path to the data set MTBLS2
> mtbls_ftp_path("MTBLS2")
[1] "ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS2/"
> 
> ## Retrieve available files (and directories) for the data set MTBLS2
> mtbls_list_files("MTBLS2")
[1] "FILES"                                                     
[2] "a_MTBLS2_metabolite_profiling_mass_spectrometry.txt"       
[3] "files-all.json"                                            
[4] "i_Investigation.txt"                                       
[5] "m_MTBLS2_metabolite_profiling_mass_spectrometry_v2_maf.tsv"
[6] "s_MTBLS2.txt"                                              
> 
> ## Retrieve the available assay files (file names starting with "a_").
> afiles <- mtbls_list_files("MTBLS2", pattern = "^a_")
> afiles
[1] "a_MTBLS2_metabolite_profiling_mass_spectrometry.txt"
> 
> ## Read the content of one file
> a <- read.table(paste0(mtbls_ftp_path("MTBLS2"), afiles[1L]),
+     header = TRUE, sep = "\t", check.names = FALSE)
Warning in file(file, "rt") :
  URL 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS2/a_MTBLS2_metabolite_profiling_mass_spectrometry.txt': status was 'Failure when receiving data from the peer'
Error in file(file, "rt") : 
  cannot open the connection to 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS2/a_MTBLS2_metabolite_profiling_mass_spectrometry.txt'
Calls: read.table -> file
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:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_MsBackendMetaboLights.R:167:1'): (code run outside of `test_that()`) ──
  Error in `file(file, "rt")`: cannot open the connection to 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS2/a_MTBLS2_metabolite_profiling_mass_spectrometry.txt'
  Backtrace:
      ▆
   1. └─MsBackendMetaboLights:::.mtbls_assay_list("MTBLS2") at test_MsBackendMetaboLights.R:167:1
   2.   └─base::lapply(...)
   3.     └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
   4.       └─utils::read.table(...)
   5.         └─base::file(file, "rt")
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 51 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘MsBackendMetaboLights.Rmd’ using rmarkdown

Quitting from lines 201-203 [unnamed-chunk-12] (MsBackendMetaboLights.Rmd)
Error: processing vignette 'MsBackendMetaboLights.Rmd' failed with diagnostics:
Failed to connect to MetaboLights. No internet connection? Does the data set "MTBLS39" exist?
 - cannot open the connection
--- failed re-building ‘MsBackendMetaboLights.Rmd’

SUMMARY: processing the following file failed:
  ‘MsBackendMetaboLights.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MsBackendMetaboLights.Rcheck/00check.log’
for details.