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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMetaboLights_1.0.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsBackendMetaboLights.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 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 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: 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")
Used data files from the assay's column "Raw Spectral Data File" since none were available in column "Derived Spectral Data File".
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063B.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063B.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/MN063B.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC5145
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063B.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063B.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073A.cdf'
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073A.cdf' produced error:
  Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083C.cdf'
Error in bfcrpath(bfc, paste0(fpath, ffiles), fname = "exact") : 
  not all 'rnames' found or unique.
Calls: backendInitialize ... .local -> .mtbls_data_files -> bfcrpath -> bfcrpath
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:
  mz(x[1:50]) not equal to mz(res[1:50]).
  Attributes: < Component "listData": Component 1: Numeric: lengths (389, 388) differ >
  Attributes: < Component "listData": Component 2: Numeric: lengths (393, 387) differ >
  Attributes: < Component "listData": Component 3: Numeric: lengths (371, 367) differ >
  Attributes: < Component "listData": Component 4: Numeric: lengths (375, 370) differ >
  Attributes: < Component "listData": Component 5: Numeric: lengths (392, 383) differ >
  Attributes: < Component "listData": Component 6: Numeric: lengths (397, 377) differ >
  Attributes: < Component "listData": Component 7: Numeric: lengths (369, 366) differ >
  Attributes: < Component "listData": Component 8: Numeric: lengths (355, 394) differ >
  Attributes: < Component "listData": Component 9: Numeric: lengths (395, 384) differ >
  ...
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ]
  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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsBackendMetaboLights.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendMetaboLights
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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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

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 1 | WARN 3 | SKIP 0 | PASS 66 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_MsBackendMetaboLights.R:67:5'): mtbls_sync works ─────────────
mz(x[1:50]) not equal to mz(res[1:50]).
Attributes: < Component "listData": Component 1: Numeric: lengths (389, 388) differ >
Attributes: < Component "listData": Component 2: Numeric: lengths (393, 387) differ >
Attributes: < Component "listData": Component 3: Numeric: lengths (371, 367) differ >
Attributes: < Component "listData": Component 4: Numeric: lengths (375, 370) differ >
Attributes: < Component "listData": Component 5: Numeric: lengths (392, 383) differ >
Attributes: < Component "listData": Component 6: Numeric: lengths (397, 377) differ >
Attributes: < Component "listData": Component 7: Numeric: lengths (369, 366) differ >
Attributes: < Component "listData": Component 8: Numeric: lengths (355, 394) differ >
Attributes: < Component "listData": Component 9: Numeric: lengths (395, 384) differ >
...

[ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ]
Error: Test failures
Execution halted