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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MsBackendMetaboLights_1.4.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MsBackendMetaboLights.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendMetaboLights/DESCRIPTION’ ... OK
* this is package ‘MsBackendMetaboLights’ version ‘1.4.2’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
MsBackendMetaboLights 9.670  1.040  88.058
MetaboLights-utils    0.432  0.018  81.103
* 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:
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─ProtGenerics::backendInitialize(MsBackendMetaboLights(), mtblsId = "MTBLS100")
    7. └─MsBackendMetaboLights::backendInitialize(...)
    8.   └─MsBackendMetaboLights (local) .local(object, ...)
    9.     └─MsBackendMetaboLights:::.mtbls_data_files(...)
   10.       └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
   11.         └─base::lapply(...)
   12.           └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
   13.             └─MsBackendMetaboLights::retry(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 77 ]
  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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MsBackendMetaboLights.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MsBackendMetaboLights
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MsBackendMetaboLights’ ...
** this is package ‘MsBackendMetaboLights’ version ‘1.4.2’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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.

> #' 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")
Saving _problems/test_MsBackendMetaboLights-27.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 77 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_MsBackendMetaboLights.R:26:5'): backendInitialize,MsBackendMetaboLights works ──
`backendInitialize(MsBackendMetaboLights(), mtblsId = "MTBLS100")` threw an error with unexpected message.
Expected match: "No files matching"
Actual message: "cannot open the connection to 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS100/a_MTBLS100_dwhsaliva_metabolite_profiling_NMR_spectroscopy.txt'"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_MsBackendMetaboLights.R:26:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─ProtGenerics::backendInitialize(MsBackendMetaboLights(), mtblsId = "MTBLS100")
  7. └─MsBackendMetaboLights::backendInitialize(...)
  8.   └─MsBackendMetaboLights (local) .local(object, ...)
  9.     └─MsBackendMetaboLights:::.mtbls_data_files(...)
 10.       └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
 11.         └─base::lapply(...)
 12.           └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
 13.             └─MsBackendMetaboLights::retry(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 77 ]
Error:
! Test failures.
Execution halted