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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsQuality_1.8.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MsQuality.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsQuality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsQuality’ version ‘1.8.1’
* 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 ‘MsQuality’ 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 ... NOTE
transformIntoMzQC : <anonymous>: no visible global function definition
  for ‘MzQCrunQuality’
transformIntoMzQC : <anonymous>: no visible global function definition
  for ‘MzQCmetadata’
transformIntoMzQC : <anonymous>: no visible global function definition
  for ‘MzQCinputFile’
transformIntoMzQC : <anonymous>: no visible global function definition
  for ‘MzQCmzQC’
transformIntoMzQC : <anonymous>: no visible global function definition
  for ‘MzQCDateTime’
Undefined global functions or variables:
  MzQCDateTime MzQCinputFile MzQCmetadata MzQCmzQC MzQCrunQuality
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
calculateMetricsFromMsExperiment 7.714  2.380   5.848
calculateMetrics                 8.174  1.352   9.802
calculateMetricsFromSpectra      5.449  1.680   4.928
plotMetric                       4.471  1.336   3.964
plotMetricTibble                 4.283  1.520   3.617
* 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:
      raw_file, file_format)), analysisSoftware = list(software)), 
      qualityMetrics = qc_metric_i)`: could not find function "MzQCrunQuality"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test_function_calculateMetrics_from_Spectra.R:1057:5
   2. │ └─base::withCallingHandlers(...)
   3. └─MsQuality::calculateMetrics(...)
   4.   └─MsQuality::calculateMetricsFromSpectra(...)
   5.     └─MsQuality:::transformIntoMzQC(spectra_metrics)
   6.       └─base::lapply(...)
   7.         └─MsQuality (local) FUN(X[[i]], ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 598 ]
  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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MsQuality.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsQuality
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘MsQuality’ ...
** this is package ‘MsQuality’ version ‘1.8.1’
** using staged installation
** R
** data
** inst
** 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 (MsQuality)

R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
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.

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.

> library("testthat")
> library("MsQuality")
> library("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
> library("MsExperiment")
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

> library("msdata")
> library("S4Vectors")
> 
> test_check("MsQuality")
trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
Content type 'application/json; charset=utf-8' length 7624 bytes
==================================================
downloaded 7624 bytes

trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.197/psi-ms.obo'
Content type 'application/octet-stream' length 1011047 bytes (987 KB)
==================================================
downloaded 987 KB

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 598 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_function_calculateMetrics_from_Spectra.R:623:4'): calculateMetricsFromSpectra, format = 'mzQC'. ──
Error in `MzQCrunQuality(metadata = MzQCmetadata(label = raw_file, inputFiles = list(MzQCinputFile(basename(raw_file), 
    raw_file, file_format)), analysisSoftware = list(software)), 
    qualityMetrics = qc_metric_i)`: could not find function "MzQCrunQuality"
Backtrace:
    ▆
 1. └─MsQuality::calculateMetricsFromSpectra(...) at test_function_calculateMetrics_from_Spectra.R:623:4
 2.   └─MsQuality:::transformIntoMzQC(spectra_metrics)
 3.     └─base::lapply(...)
 4.       └─MsQuality (local) FUN(X[[i]], ...)
── Error ('test_function_calculateMetrics_from_Spectra.R:851:5'): calculateMetricsFromMsExperiment, format = 'mzQC'. ──
Error in `MzQCrunQuality(metadata = MzQCmetadata(label = raw_file, inputFiles = list(MzQCinputFile(basename(raw_file), 
    raw_file, file_format)), analysisSoftware = list(software)), 
    qualityMetrics = qc_metric_i)`: could not find function "MzQCrunQuality"
Backtrace:
    ▆
 1. ├─base::suppressWarnings(...) at test_function_calculateMetrics_from_Spectra.R:851:5
 2. │ └─base::withCallingHandlers(...)
 3. └─MsQuality::calculateMetricsFromMsExperiment(...)
 4.   └─MsQuality::calculateMetricsFromSpectra(...)
 5.     └─MsQuality:::transformIntoMzQC(spectra_metrics)
 6.       └─base::lapply(...)
 7.         └─MsQuality (local) FUN(X[[i]], ...)
── Error ('test_function_calculateMetrics_from_Spectra.R:1057:5'): calculateMetrics, format = 'mzQC'. ──
Error in `MzQCrunQuality(metadata = MzQCmetadata(label = raw_file, inputFiles = list(MzQCinputFile(basename(raw_file), 
    raw_file, file_format)), analysisSoftware = list(software)), 
    qualityMetrics = qc_metric_i)`: could not find function "MzQCrunQuality"
Backtrace:
    ▆
 1. ├─base::suppressWarnings(...) at test_function_calculateMetrics_from_Spectra.R:1057:5
 2. │ └─base::withCallingHandlers(...)
 3. └─MsQuality::calculateMetrics(...)
 4.   └─MsQuality::calculateMetricsFromSpectra(...)
 5.     └─MsQuality:::transformIntoMzQC(spectra_metrics)
 6.       └─base::lapply(...)
 7.         └─MsQuality (local) FUN(X[[i]], ...)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 598 ]
Error: Test failures
Execution halted