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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:artMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings artMS_1.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/artMS.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘artMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘artMS’ version ‘1.29.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘artMS’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘artMS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: artmsQuantification
> ### Title: Relative quantification using MSstats
> ### Aliases: artmsQuantification
> ### Keywords: driver, function main,
> 
> ### ** Examples
> 
> # Recommended
> # artmsQuantification(yaml_config_file = "your-config-file.yaml")
> 
> # Example to test this function using the example dataset available in artMS
> # Step 1: Add evidence, keys, and contrast to configuration object
> artms_data_ph_config$files$evidence <- artms_data_ph_evidence
> artms_data_ph_config$files$keys <- artms_data_ph_keys
> artms_data_ph_config$files$contrasts <- artms_data_ph_contrast
> 
> # Step 2: Run the quantification step
> quant_results <- artmsQuantification(yaml_config_file = artms_data_ph_config, 
+                                      data_object = TRUE, 
+                                      display_msstats = FALSE,
+                                      printPDF = FALSE,
+                                      printTables = FALSE)
--------------------------------------------
artMS: Relative Quantification using MSstats
--------------------------------------------
>> Reading the configuration file
>> LOADING DATA 
>> MERGING FILES 
>> CONVERT Intensity values < 1 to NA
>> FILTERING 
-- Contaminants CON__|REV__ removed
-- Removing protein groups
-- Use <Leading.razor.protein> as Protein ID
>> CONVERTING THE DATA TO MSSTATS FORMAT 
-- Selecting Sequence Type: MaxQuant 'Modified.sequence' column
	(+) <Fraction> column added (with value 1, MSstats requirement)
-- Adding NA values for missing values (required by MSstats) 
>> RUNNING MSstats (it usually takes a 'long' time: please, be patient)
	(MSstats messages are turned off. Select <display_msstats = TRUE> to activate MSstats outputs)
Error in `[.data.table`(input, , `:=`(n_obs, sum(Intensity > min_intensity,  : 
  attempt access index 13/13 in VECTOR_ELT
Calls: artmsQuantification ... withVisible -> suppressMessages -> withCallingHandlers
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:
    8.   └─artMS:::.artms_runMSstats(...)
    9.     └─MSstats::dataProcess(...)
   10.       └─MSstats::MSstatsPrepareForDataProcess(raw, logTrans, fix_missing)
   11.         ├─MSstats:::.checkDataValidity(input, fix_missing = fix_missing)
   12.         └─MSstats:::.checkDataValidity(input, fix_missing = fix_missing)
   13.           └─MSstats (local) .local(input, ...)
   14.             └─MSstatsConvert::MSstatsBalancedDesign(...)
   15.               └─MSstatsConvert:::.filterFewMeasurements(...)
   16.                 ├─...[]
   17.                 └─data.table:::`[.data.table`(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  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-3.23-bioc/meat/artMS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL artMS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘artMS’ ...
** this is package ‘artMS’ version ‘1.29.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (artMS)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-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(artMS)

> 
> test_check("artMS")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-evidence.R:19:3'): Check artmsQuantification() output ──────────
Error in ``[.data.table`(input, , `:=`(n_obs, sum(Intensity > min_intensity, na.rm = TRUE)), by = feature_columns)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
     ▆
  1. └─artMS::artmsQuantification(...) at test-evidence.R:19:3
  2.   ├─utils::capture.output(...)
  3.   │ └─base::withVisible(...elt(i))
  4.   ├─base::suppressMessages(...)
  5.   │ └─base::withCallingHandlers(...)
  6.   ├─base::suppressWarnings(...)
  7.   │ └─base::withCallingHandlers(...)
  8.   └─artMS:::.artms_runMSstats(...)
  9.     └─MSstats::dataProcess(...)
 10.       └─MSstats::MSstatsPrepareForDataProcess(raw, logTrans, fix_missing)
 11.         ├─MSstats:::.checkDataValidity(input, fix_missing = fix_missing)
 12.         └─MSstats:::.checkDataValidity(input, fix_missing = fix_missing)
 13.           └─MSstats (local) .local(input, ...)
 14.             └─MSstatsConvert::MSstatsBalancedDesign(...)
 15.               └─MSstatsConvert:::.filterFewMeasurements(...)
 16.                 ├─...[]
 17.                 └─data.table:::`[.data.table`(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
Error:
! Test failures.
Execution halted