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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MsBackendMetaboLights.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MsBackendMetaboLights_1.0.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MsBackendMetaboLights.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MsBackendMetaboLights/DESCRIPTION' ... OK
* this is package 'MsBackendMetaboLights' version '1.0.0'
* 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 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 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
> 
> ### ** 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:
   2.   ├─BiocFileCache::bfcrpath(bfc, paste0(fpath, ffiles), fname = "exact")
   3.   └─BiocFileCache::bfcrpath(bfc, paste0(fpath, ffiles), fname = "exact")
  ── Error ('test_MsBackendMetaboLights.R:168:1'): (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/MTBLS123/a_MTBLS123_monr_muscle_NMRspectroscopy.txt'
  Backtrace:
      ▆
   1. └─MsBackendMetaboLights:::.mtbls_assay_list("MTBLS123") at test_MsBackendMetaboLights.R:168:1
   2.   └─base::lapply(...)
   3.     └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
   4.       └─utils::read.table(...)
   5.         └─base::file(file, "rt")
  
  [ FAIL 4 | WARN 5 | SKIP 0 | PASS 31 ]
  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
  'F:/biocbuild/bbs-3.20-bioc/meat/MsBackendMetaboLights.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MsBackendMetaboLights
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'MsBackendMetaboLights' ...
** using staged installation
** R
** 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 (MsBackendMetaboLights)

R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

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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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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 4 | WARN 5 | SKIP 0 | PASS 31 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_MsBackendMetaboLights.R:65:5'): mtbls_sync works ───────────────
Error in `file(file, "rt")`: cannot open the connection to 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/a_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry.txt'
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.           └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
  7.             └─base::lapply(...)
  8.               └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
  9.                 └─utils::read.table(...)
 10.                   └─base::file(file, "rt")
── Failure ('test_MsBackendMetaboLights.R:90:5'): .mtbls_data_files and .mtbls_data_files_offline works ──
`.mtbls_data_files(mtblsId = "MTBLS2", assayName = "does not exist")` threw an error with unexpected message.
Expected match: "Not all assay names"
Actual message: "Failed to connect to MetaboLights. No internet connection? Does the data set \"MTBLS2\" exist?\n - cannot open the connection"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_MsBackendMetaboLights.R:90:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─MsBackendMetaboLights:::.mtbls_data_files(...)
  7.   └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
  8.     └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
  9.       └─base::tryCatch(...)
 10.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.             └─value[[3L]](cond)
── Error ('test_MsBackendMetaboLights.R:106:5'): .mtbls_data_files and .mtbls_data_files_offline works ──
Error in `bfcrpath(bfc, paste0(fpath, ffiles), fname = "exact")`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─MsBackendMetaboLights:::.mtbls_data_files("MTBLS39", pattern = "63A.cdf") at test_MsBackendMetaboLights.R:106:5
 2.   ├─BiocFileCache::bfcrpath(bfc, paste0(fpath, ffiles), fname = "exact")
 3.   └─BiocFileCache::bfcrpath(bfc, paste0(fpath, ffiles), fname = "exact")
── Error ('test_MsBackendMetaboLights.R:168:1'): (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/MTBLS123/a_MTBLS123_monr_muscle_NMRspectroscopy.txt'
Backtrace:
    ▆
 1. └─MsBackendMetaboLights:::.mtbls_assay_list("MTBLS123") at test_MsBackendMetaboLights.R:168:1
 2.   └─base::lapply(...)
 3.     └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
 4.       └─utils::read.table(...)
 5.         └─base::file(file, "rt")

[ FAIL 4 | WARN 5 | SKIP 0 | PASS 31 ]
Error: Test failures
Execution halted