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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MsBackendMetaboLights.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MsBackendMetaboLights_1.1.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MsBackendMetaboLights.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 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 '1.1.0'
* 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 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 ... 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: MsBackendMetaboLights
> ### Title: MsBackend representing MS data from MetaboLights
> ### Aliases: MsBackendMetaboLights MsBackendMetaboLights-class
> ###   backendInitialize,MsBackendMetaboLights-method
> ###   backendMerge,MsBackendMetaboLights-method
> ###   backendRequiredSpectraVariables,MsBackendMetaboLights-method
> ###   mtbls_sync
> 
> ### ** Examples
> 
> 
> library(MsBackendMetaboLights)
> 
> ## List files of a MetaboLights data set
> mtbls_list_files("MTBLS39")
[1] "FILES"                                                                                                          
[2] "a_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry.txt"       
[3] "i_Investigation.txt"                                                                                            
[4] "m_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry_v2_maf.tsv"
[5] "metexplore_mapping.json"                                                                                        
[6] "s_MTBLS39.txt"                                                                                                  
> 
> ## Initialize a MsBackendMetaboLights representing all MS data files of
> ## the data set with the ID "MTBLS39". This will download and cache all
> ## files and subsequently load and represent them in R.
> 
> be <- backendInitialize(MsBackendMetaboLights(), "MTBLS39")
Warning in file(file, "rt") :
  URL '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': 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/MTBLS39/a_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry.txt'
Calls: backendInitialize ... .mtbls_assay_list -> lapply -> FUN -> read.table -> file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
MetaboLights-utils 0.48   0.05    7.22
* 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: Failed to connect to MetaboLights. No internet connection? Does the data set "MTBLS39" exist?
   - cannot open the connection
  Backtrace:
      ▆
   1. └─MsBackendMetaboLights:::.mtbls_data_files(...) at test_MsBackendMetaboLights.R:122:5
   2.   └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
   3.     └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
   4.       └─base::tryCatch(...)
   5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.             └─value[[3L]](cond)
  
  [ FAIL 3 | WARN 6 | SKIP 0 | PASS 55 ]
  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, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/MsBackendMetaboLights.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL MsBackendMetaboLights
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'MsBackendMetaboLights' ...
** this is package 'MsBackendMetaboLights' version '1.1.0'
** 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 Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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Type 'license()' or 'licence()' for distribution details.

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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 3 | WARN 6 | SKIP 0 | PASS 55 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_MsBackendMetaboLights.R:65:5'): mtbls_sync works ───────────────
Error in `bfcrpath(bfc, paste0(fpath, ffiles), 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.           ├─BiocFileCache::bfcrpath(bfc, paste0(fpath, ffiles), fname = "exact")
 7.           └─BiocFileCache::bfcrpath(bfc, paste0(fpath, ffiles), fname = "exact")
── 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: "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. ├─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.     └─base::lapply(...)
  9.       └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
 10.         └─utils::read.table(...)
 11.           └─base::file(file, "rt")
── Error ('test_MsBackendMetaboLights.R:122:5'): .mtbls_data_files and .mtbls_data_files_offline works ──
Error: Failed to connect to MetaboLights. No internet connection? Does the data set "MTBLS39" exist?
 - cannot open the connection
Backtrace:
    ▆
 1. └─MsBackendMetaboLights:::.mtbls_data_files(...) at test_MsBackendMetaboLights.R:122:5
 2.   └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
 3.     └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
 4.       └─base::tryCatch(...)
 5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.             └─value[[3L]](cond)

[ FAIL 3 | WARN 6 | SKIP 0 | PASS 55 ]
Error: Test failures
Execution halted