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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MsBackendMetaboLights_1.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MsBackendMetaboLights.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 ‘MsBackendMetaboLights/DESCRIPTION’ ... OK
* this is package ‘MsBackendMetaboLights’ version ‘1.3.1’
* 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 ... 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 ... 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 ‘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 mtbls_delete_cache
> 
> ### ** 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] "HASHES"                                                    
[3] "METADATA_REVISIONS"                                        
[4] "a_MTBLS2_metabolite_profiling_mass_spectrometry.txt"       
[5] "i_Investigation.txt"                                       
[6] "m_MTBLS2_metabolite_profiling_mass_spectrometry_v2_maf.tsv"
[7] "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:
    3.     └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
    4.       └─MsBackendMetaboLights::mtbls_sync_data_files(...)
    5.         └─MsBackendMetaboLights:::.mtbls_data_files(...)
    6.           ├─base::unlist(...)
    7.           └─base::lapply(...)
    8.             └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
    9.               ├─utils::capture.output(...)
   10.               │ └─base::withVisible(...elt(i))
   11.               ├─base::suppressMessages(...)
   12.               │ └─base::withCallingHandlers(...)
   13.               └─MsBackendMetaboLights:::.retry(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MsBackendMetaboLights.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MsBackendMetaboLights
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘MsBackendMetaboLights’ ...
** this is package ‘MsBackendMetaboLights’ version ‘1.3.1’
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (MsBackendMetaboLights)

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
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> #' MetaboLights ID: MTBLS8735
> #' ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8735
> 
> library(testthat)
> library(MsBackendMetaboLights)
Loading required package: Spectra
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: BiocParallel
> 
> test_check("MsBackendMetaboLights")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_MsBackendMetaboLights.R:65:5'): mtbls_sync works ───────────────
Error in `bfcrpath(bfc, paste0(fpath, z), fname = "exact")`: not all 'rnames' found or unique.
Backtrace:
     ▆
  1. └─MsBackendMetaboLights::mtbls_sync(x, offline = FALSE) at test_MsBackendMetaboLights.R:65:5
  2.   └─base::lapply(...)
  3.     └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
  4.       └─MsBackendMetaboLights::mtbls_sync_data_files(...)
  5.         └─MsBackendMetaboLights:::.mtbls_data_files(...)
  6.           ├─base::unlist(...)
  7.           └─base::lapply(...)
  8.             └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
  9.               ├─utils::capture.output(...)
 10.               │ └─base::withVisible(...elt(i))
 11.               ├─base::suppressMessages(...)
 12.               │ └─base::withCallingHandlers(...)
 13.               └─MsBackendMetaboLights:::.retry(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
Error: Test failures
Execution halted