Multiple platform build/check report for BioC 3.22 - CHECK results for MSstatsConvert on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4843
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4631
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4575
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4576
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for MSstatsConvert on kjohnson3

To the developers/maintainers of the MSstatsConvert package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsConvert.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: MSstatsConvert

Version: 1.19.3

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsConvert_1.19.3.tar.gz

StartedAt: 2025-09-29 20:34:45 -0400 (Mon, 29 Sep 2025)

EndedAt: 2025-09-29 20:35:07 -0400 (Mon, 29 Sep 2025)

EllapsedTime: 21.3 seconds

RetCode: 0

Status: OK

CheckDir: MSstatsConvert.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsConvert_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MSstatsConvert.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK
* this is package ‘MSstatsConvert’ version ‘1.19.3’
* 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 ‘MSstatsConvert’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... INFO
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    tinytest   6.0Mb
* 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 whether startup messages can be suppressed ... 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
.checkAnomalySkew: no visible global function definition for ‘.’
.checkAnomalySkew: no visible binding for global variable
  ‘AnomalyScores’
.checkAnomalySkew: no visible binding for global variable ‘PSM’
.checkFeatureCoverage: no visible global function definition for ‘.’
.checkFeatureCoverage: no visible binding for global variable
  ‘Intensity’
.checkFeatureCoverage: no visible binding for global variable ‘Feature’
.checkFeatureOutliers: no visible binding for global variable
  ‘is_outlier’
.checkFeatureOutliers: no visible binding for global variable
  ‘Intensity’
.checkFeatureOutliers: no visible binding for global variable
  ‘mean_Intensity’
.checkFeatureOutliers: no visible binding for global variable
  ‘sd_Intensity’
.checkFeatureOutliers: no visible global function definition for ‘.’
.checkFeatureOutliers: no visible binding for global variable ‘Feature’
.checkFeatureSD: no visible global function definition for ‘.’
.checkFeatureSD: no visible global function definition for ‘sd’
.checkFeatureSD: no visible binding for global variable ‘Intensity’
.checkFeatureSD: no visible binding for global variable ‘Feature’
.checkIntensityDistribution: no visible global function definition for
  ‘sd’
.cleanDIANNAddMissingColumns: no visible binding for global variable
  ‘PrecursorMz’
.cleanDIANNAddMissingColumns: no visible binding for global variable
  ‘FragmentInfo’
.cleanDIANNCleanAndFilterData: no visible binding for global variable
  ‘FragmentIon’
.cleanDIANNProcessFragmentInfo: no visible binding for global variable
  ‘FragmentInfo’
.cleanDIANNProcessFragmentInfo: no visible binding for global variable
  ‘FragmentIon’
.cleanDIANNProcessFragmentInfo: no visible binding for global variable
  ‘ProductCharge’
.cleanDIANNProcessQuantificationColumns: no visible binding for global
  variable ‘FragmentQuantCorrected’
.cleanDIANNRenameColumns: no visible binding for global variable
  ‘PeptideSequence’
.cleanRawPhilosopher: no visible binding for global variable ‘Run’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘Intensity’
.prepareSpectronautAnomalyInput: no visible global function definition
  for ‘.’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘Fragment’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘count’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘ProteinName’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘feature_rank’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘MeanAbundance’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘..cols’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘PSM’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘Order’
.runAnomalyModel : <anonymous>: no visible binding for global variable
  ‘..quality_metrics’
.summarizeMultipleMeasurements: no visible binding for global variable
  ‘row_id’
.summarizeMultipleMeasurements: no visible global function definition
  for ‘.’
.summarizeMultiplePSMs: no visible binding for global variable ‘Purity’
.summarizeMultiplePSMs: no visible binding for global variable
  ‘PeptideProphet.Probability’
.validateMSstatsConverterParameters: no visible global function
  definition for ‘modifyList’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘DetectionQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalQValue’
MSstatsAnomalyScores: no visible binding for global variable
  ‘..subset_cols’
SkylinetoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
SpectronauttoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
pearson_skewness: no visible global function definition for ‘sd’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘Run’
Undefined global functions or variables:
  . ..cols ..quality_metrics ..subset_cols AnomalyScores
  DetectionQValue Feature Fragment FragmentInfo FragmentIon
  FragmentQuantCorrected GlobalPGQValue GlobalQValue Intensity
  LibPGQValue LibQValue MeanAbundance Order PSM
  PeptideProphet.Probability PeptideSequence PrecursorMz ProductCharge
  ProteinName Purity Run count feature_rank is_outlier mean_Intensity
  modifyList row_id sd sd_Intensity
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-getFullDesign.Rd':
  ‘`feature_col`’ ‘`measurement_col`’

Documented arguments not in \usage in Rd file 'dot-mergeAnnotation.Rd':
  ‘data.table’

Documented arguments not in \usage in Rd file 'dot-sharedParametersAmongConverters.Rd':
  ‘removeFewMeasurements’ ‘useUniquePeptide’ ‘summaryforMultipleRows’
  ‘removeProtein_with1Feature’ ‘removeProtein_with1Peptide’
  ‘removeOxidationMpeptides’ ‘removeMpeptides’ ‘use_log_file’ ‘append’
  ‘verbose’ ‘log_file_path’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/MSstatsConvert.Rcheck/00check.log’
for details.

Installation output

MSstatsConvert.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsConvert
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘MSstatsConvert’ ...
** this is package ‘MSstatsConvert’ version ‘1.19.3’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c isolation_forest.cpp -o isolation_forest.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o MSstatsConvert.so RcppExports.o isolation_forest.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-MSstatsConvert/00new/MSstatsConvert/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsConvert)

Tests output

MSstatsConvert.Rcheck/tests/tinytest.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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.

> 
> if (requireNamespace("tinytest", quietly = TRUE)) {
+     MSstatsConvert::MSstatsLogsSettings(FALSE, FALSE, TRUE)
+     tinytest::test_package("MSstatsConvert")
+ }

test_MSstatsConvert.R.........    0 tests    
test_MSstatsConvert.R.........    0 tests    
test_MSstatsConvert.R.........    0 tests    
test_MSstatsConvert.R.........    0 tests    
test_MSstatsConvert.R.........    0 tests    
test_MSstatsConvert.R.........    0 tests    
test_MSstatsConvert.R.........    0 tests    
test_MSstatsConvert.R.........    1 tests [0;32mOK[0m 
test_MSstatsConvert.R.........    2 tests [0;32mOK[0m 
test_MSstatsConvert.R.........    3 tests [0;32mOK[0m 
test_MSstatsConvert.R.........    4 tests [0;32mOK[0m 
test_MSstatsConvert.R.........    5 tests [0;32mOK[0m 
test_MSstatsConvert.R.........    6 tests [0;32mOK[0m [0;36m25ms[0m

test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    INFO  [2025-09-29 20:34:58] ** Using annotation extracted from quantification data.
INFO  [2025-09-29 20:34:58] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    1 tests [0;32mOK[0m INFO  [2025-09-29 20:34:58] ** Using provided annotation.
INFO  [2025-09-29 20:34:58] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    2 tests [0;32mOK[0m 
test_annotation.R.............    2 tests [0;32mOK[0m INFO  [2025-09-29 20:34:58] ** Using provided annotation.
INFO  [2025-09-29 20:34:58] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    3 tests [0;32mOK[0m INFO  [2025-09-29 20:34:58] ** Using provided annotation.
INFO  [2025-09-29 20:34:58] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    4 tests [0;32mOK[0m 
test_annotation.R.............    4 tests [0;32mOK[0m 
test_annotation.R.............    4 tests [0;32mOK[0m 
test_annotation.R.............    5 tests [0;32mOK[0m INFO  [2025-09-29 20:34:58] ** Run annotation merged with quantification data.

test_annotation.R.............    6 tests [0;32mOK[0m INFO  [2025-09-29 20:34:58] ** Using provided annotation.
INFO  [2025-09-29 20:34:58] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    6 tests [0;32mOK[0m INFO  [2025-09-29 20:34:58] ** Run annotation merged with quantification data.

test_annotation.R.............    7 tests [0;32mOK[0m INFO  [2025-09-29 20:34:58] ** Using provided annotation.
INFO  [2025-09-29 20:34:58] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    7 tests [0;32mOK[0m 
test_annotation.R.............    8 tests [0;32mOK[0m INFO  [2025-09-29 20:34:58] ** Using provided annotation.
INFO  [2025-09-29 20:34:58] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    8 tests [0;32mOK[0m 
test_annotation.R.............    9 tests [0;32mOK[0m 
test_annotation.R.............   10 tests [0;32mOK[0m INFO  [2025-09-29 20:34:58] ** Using provided annotation.

test_annotation.R.............   11 tests [0;32mOK[0m [0;36m28ms[0m

test_balanced_design.R........    0 tests    
test_balanced_design.R........    0 tests    
test_balanced_design.R........    0 tests    
test_balanced_design.R........    0 tests    
test_balanced_design.R........    0 tests    
test_balanced_design.R........    0 tests    
test_balanced_design.R........    0 tests    
test_balanced_design.R........    0 tests    
test_balanced_design.R........    1 tests [0;32mOK[0m 
test_balanced_design.R........    2 tests [0;32mOK[0m 
test_balanced_design.R........    3 tests [0;32mOK[0m 
test_balanced_design.R........    3 tests [0;32mOK[0m 
test_balanced_design.R........    3 tests [0;32mOK[0m 
test_balanced_design.R........    3 tests [0;32mOK[0m 
test_balanced_design.R........    4 tests [0;32mOK[0m 
test_balanced_design.R........    4 tests [0;32mOK[0m 
test_balanced_design.R........    4 tests [0;32mOK[0m 
test_balanced_design.R........    4 tests [0;32mOK[0m 
test_balanced_design.R........    4 tests [0;32mOK[0m 
test_balanced_design.R........    4 tests [0;32mOK[0m 
test_balanced_design.R........    4 tests [0;32mOK[0m 
test_balanced_design.R........    5 tests [0;32mOK[0m 
test_balanced_design.R........    5 tests [0;32mOK[0m 
test_balanced_design.R........    6 tests [0;32mOK[0m 
test_balanced_design.R........    7 tests [0;32mOK[0m 
test_balanced_design.R........    7 tests [0;32mOK[0m 
test_balanced_design.R........    7 tests [0;32mOK[0m 
test_balanced_design.R........    7 tests [0;32mOK[0m 
test_balanced_design.R........    7 tests [0;32mOK[0m 
test_balanced_design.R........    7 tests [0;32mOK[0m 
test_balanced_design.R........    7 tests [0;32mOK[0m 
test_balanced_design.R........    7 tests [0;32mOK[0m 
test_balanced_design.R........    8 tests [0;32mOK[0m 
test_balanced_design.R........    9 tests [0;32mOK[0m 
test_balanced_design.R........   10 tests [0;32mOK[0m 
test_balanced_design.R........   11 tests [0;32mOK[0m [0;36m19ms[0m

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2025-09-29 20:34:58] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-09-29 20:34:58] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-09-29 20:34:58] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2025-09-29 20:34:58] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-09-29 20:34:58] ** Using selected fragments and peptides.
INFO  [2025-09-29 20:34:58] ** Extracted the data from selected fragments and/or peptides.
INFO  [2025-09-29 20:34:58] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-09-29 20:34:58] ** Using selected fragments and peptides.
INFO  [2025-09-29 20:34:58] ** Extracted the data from selected fragments and/or peptides.
INFO  [2025-09-29 20:34:58] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-09-29 20:34:58] ** Using selected fragments.
INFO  [2025-09-29 20:34:58] ** Extracted the data from selected fragments and/or peptides.
INFO  [2025-09-29 20:34:58] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    1 tests [0;32mOK[0m 
test_cleanRaw.R...............    2 tests [0;32mOK[0m 
test_cleanRaw.R...............    3 tests [0;32mOK[0m 
test_cleanRaw.R...............    4 tests [0;32mOK[0m 
test_cleanRaw.R...............    5 tests [0;32mOK[0m 
test_cleanRaw.R...............    6 tests [0;32mOK[0m 
test_cleanRaw.R...............    7 tests [0;32mOK[0m 
test_cleanRaw.R...............    8 tests [0;32mOK[0m 
test_cleanRaw.R...............    9 tests [0;32mOK[0m 
test_cleanRaw.R...............    9 tests [0;32mOK[0m 
test_cleanRaw.R...............    9 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............    9 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2025-09-29 20:34:59] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2025-09-29 20:34:59] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2025-09-29 20:34:59] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests [0;32mOK[0m 
test_cleanRaw.R...............   10 tests [0;32mOK[0m 
test_cleanRaw.R...............   11 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2025-09-29 20:34:59] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............   12 tests [0;32mOK[0m 
test_cleanRaw.R...............   13 tests [0;32mOK[0m 
test_cleanRaw.R...............   13 tests [0;32mOK[0m 
test_cleanRaw.R...............   13 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............   13 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-09-29 20:34:59] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............   13 tests [0;32mOK[0m 
test_cleanRaw.R...............   14 tests [0;32mOK[0m 
test_cleanRaw.R...............   15 tests [0;32mOK[0m 
test_cleanRaw.R...............   15 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   15 tests [0;32mOK[0m 
test_cleanRaw.R...............   16 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   17 tests [0;32mOK[0m 
test_cleanRaw.R...............   18 tests [0;32mOK[0m 
test_cleanRaw.R...............   18 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   18 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   18 tests [0;32mOK[0m 
test_cleanRaw.R...............   19 tests [0;32mOK[0m 
test_cleanRaw.R...............   20 tests [0;32mOK[0m 
test_cleanRaw.R...............   20 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from OpenSWATH imported successfully.

test_cleanRaw.R...............   20 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from OpenSWATH cleaned successfully.

test_cleanRaw.R...............   20 tests [0;32mOK[0m 
test_cleanRaw.R...............   21 tests [0;32mOK[0m 
test_cleanRaw.R...............   22 tests [0;32mOK[0m 
test_cleanRaw.R...............   22 tests [0;32mOK[0m 
test_cleanRaw.R...............   22 tests [0;32mOK[0m 
test_cleanRaw.R...............   22 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests [0;32mOK[0m 
test_cleanRaw.R...............   23 tests [0;32mOK[0m 
test_cleanRaw.R...............   24 tests [0;32mOK[0m 
test_cleanRaw.R...............   25 tests [0;32mOK[0m 
test_cleanRaw.R...............   25 tests [0;32mOK[0m 
test_cleanRaw.R...............   25 tests [0;32mOK[0m 
test_cleanRaw.R...............   25 tests [0;32mOK[0m 
test_cleanRaw.R...............   25 tests [0;32mOK[0m 
test_cleanRaw.R...............   25 tests [0;32mOK[0m 
test_cleanRaw.R...............   25 tests [0;32mOK[0m 
test_cleanRaw.R...............   25 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests [0;32mOK[0m 
test_cleanRaw.R...............   26 tests [0;32mOK[0m 
test_cleanRaw.R...............   27 tests [0;32mOK[0m 
test_cleanRaw.R...............   28 tests [0;32mOK[0m 
test_cleanRaw.R...............   29 tests [0;32mOK[0m 
test_cleanRaw.R...............   30 tests [0;32mOK[0m 
test_cleanRaw.R...............   30 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests [0;32mOK[0m 
test_cleanRaw.R...............   30 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests [0;32mOK[0m 
test_cleanRaw.R...............   31 tests [0;32mOK[0m 
test_cleanRaw.R...............   32 tests [0;32mOK[0m 
test_cleanRaw.R...............   33 tests [0;32mOK[0m 
test_cleanRaw.R...............   33 tests [0;32mOK[0m 
test_cleanRaw.R...............   33 tests [0;32mOK[0m 
test_cleanRaw.R...............   33 tests [0;32mOK[0m 
test_cleanRaw.R...............   33 tests [0;32mOK[0m 
test_cleanRaw.R...............   33 tests [0;32mOK[0m 
test_cleanRaw.R...............   33 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests [0;32mOK[0m 
test_cleanRaw.R...............   34 tests [0;32mOK[0m 
test_cleanRaw.R...............   35 tests [0;32mOK[0m 
test_cleanRaw.R...............   36 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   37 tests [0;32mOK[0m 
test_cleanRaw.R...............   37 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from SpectroMine cleaned successfully.

test_cleanRaw.R...............   37 tests [0;32mOK[0m 
test_cleanRaw.R...............   38 tests [0;32mOK[0m 
test_cleanRaw.R...............   39 tests [0;32mOK[0m ERROR [2025-09-29 20:34:59] There is no channel intensity column in the input data, which should start with 'PSM' and end with 'Raw'.

test_cleanRaw.R...............   40 tests [0;32mOK[0m 
test_cleanRaw.R...............   40 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut cleaned successfully.

test_cleanRaw.R...............   40 tests [0;32mOK[0m 
test_cleanRaw.R...............   41 tests [0;32mOK[0m 
test_cleanRaw.R...............   42 tests [0;32mOK[0m 
test_cleanRaw.R...............   42 tests [0;32mOK[0m 
test_cleanRaw.R...............   42 tests [0;32mOK[0m 
test_cleanRaw.R...............   42 tests [0;32mOK[0m 
test_cleanRaw.R...............   42 tests [0;32mOK[0m 
test_cleanRaw.R...............   42 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   42 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut cleaned successfully.

test_cleanRaw.R...............   42 tests [0;32mOK[0m 
test_cleanRaw.R...............   43 tests [0;32mOK[0m 
test_cleanRaw.R...............   44 tests [0;32mOK[0m 
test_cleanRaw.R...............   44 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Metamorpheus imported successfully.

test_cleanRaw.R...............   44 tests [0;32mOK[0m 
test_cleanRaw.R...............   45 tests [0;32mOK[0m [0;34m0.2s[0m

test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............   15 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............   15 tests [0;32mOK[0m 
test_clean_DIANN.R............   30 tests [0;32mOK[0m [0;36m18ms[0m

test_clean_Metamorpheus.R.....    0 tests    
test_clean_Metamorpheus.R.....    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from Metamorpheus cleaned successfully.

test_clean_Metamorpheus.R.....    0 tests    
test_clean_Metamorpheus.R.....    1 tests [0;32mOK[0m 
test_clean_Metamorpheus.R.....    2 tests [0;32mOK[0m 
test_clean_Metamorpheus.R.....    3 tests [0;32mOK[0m 
test_clean_Metamorpheus.R.....    4 tests [0;32mOK[0m 
test_clean_Metamorpheus.R.....    5 tests [0;32mOK[0m 
test_clean_Metamorpheus.R.....    6 tests [0;32mOK[0m 
test_clean_Metamorpheus.R.....    7 tests [0;32mOK[0m [0;36m3ms[0m

test_clean_ProteinProspector.R    0 tests    
test_clean_ProteinProspector.R    0 tests    
test_clean_ProteinProspector.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from ProteinProspector cleaned successfully.

test_clean_ProteinProspector.R    3 tests [0;32mOK[0m [0;36m3ms[0m

test_clean_ProteomeDiscoverer.R    0 tests    
test_clean_ProteomeDiscoverer.R    0 tests    
test_clean_ProteomeDiscoverer.R    0 tests    
test_clean_ProteomeDiscoverer.R    3 tests [0;32mOK[0m 
test_clean_ProteomeDiscoverer.R    3 tests [0;32mOK[0m 
test_clean_ProteomeDiscoverer.R    3 tests [0;32mOK[0m 
test_clean_ProteomeDiscoverer.R    4 tests [0;32mOK[0m 
test_clean_ProteomeDiscoverer.R    4 tests [0;32mOK[0m 
test_clean_ProteomeDiscoverer.R    4 tests [0;32mOK[0m 
test_clean_ProteomeDiscoverer.R    7 tests [0;32mOK[0m [0;36m88ms[0m

test_converters_DIANNtoMSstatsFormat.R    0 tests    
test_converters_DIANNtoMSstatsFormat.R    0 tests    
test_converters_DIANNtoMSstatsFormat.R    0 tests    
test_converters_DIANNtoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from DIANN imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from DIANN cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using provided annotation.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** Filtering on Global Q Value < 0.01
INFO  [2025-09-29 20:34:59] ** MBR was not used to analyze the data. Now setting names and filtering
INFO  [2025-09-29 20:34:59] -- Filtering on GlobalPGQValue < 0.01
INFO  [2025-09-29 20:34:59] -- Filtering on GlobalQValue < 0.01
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Sequences containing DECOY, Decoys are removed.
INFO  [2025-09-29 20:34:59] ** Sequences containing \(UniMod\:35\) are removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] Proteins with a single feature are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
WARN  [2025-09-29 20:34:59] The following features have missing values in at least one run. AESTDDVDYIMR_2_Frag1_1,
 AESTDDVDYIMR_2_Frag2_1,
 AGWEAYLR_2_Frag1_1,
 AGWEAYLR_2_Frag2_1,
 AGWEAYLR_2_Frag3_1,
 AGWEAYLR_2_Frag4_1,
 AIDEQFGSLDELIK_2_Frag1_1,
 AIDEQFGSLDELIK_2_Frag2_1,
 AIDEQFGSLDELIK_2_Frag3_1,
 AIDEQFGSLDELIK_2_Frag4_1,
 AIDEQFGSLDELIK_2_Frag6_1,
 AIGVLPQLIIDR_3_Frag1_1,
 AIGVLPQLIIDR_3_Frag2_1,
 AIGVLPQLIIDR_3_Frag3_1,
 AIGVLPQLIIDR_3_Frag4_1,
 AIGVLPQLIIDR_3_Frag5_1,
 AIGVLPQLIIDR_3_Frag6_1,
 ALSADLAAR_2_Frag1_1,
 ALSADLAAR_2_Frag2_1,
 ANELLINVK_1_Frag1_1,
 ANELLINVK_1_Frag2_1,
 ASEEGNWSK_2_Frag1_1,
 ASEEGNWSK_2_Frag2_1,
 ASEEGNWSK_2_Frag3_1,
 ASEEGNWSK_2_Frag4_1,
 ASEEGNWSK_2_Frag5_1,
 ASEEGNWSK_2_Frag6_1,
 ATLTDLPER_2_Frag1_1,
 ATLTDLPER_2_Frag2_1,
 ATLTDLPER_2_Frag4_1,
 AVFNLASK_2_Frag1_1,
 AVFNLASK_2_Frag2_1,
 AVFNLASK_2_Frag3_1,
 AVFNLASK_2_Frag4_1,
 AVFNLASK_2_Frag5_1,
 AVFNLASK_2_Frag6_1,
 AVMC(UniMod:4)VAK_1_Frag1_1,
 AVMC(UniMod:4)VAK_1_Frag2_1,
 AVMC(UniMod:4)VAK_1_Frag3_1,
 AVMC(UniMod:4)VAK_1_Frag4_1,
 AVMC(UniMod:4)VAK_1_Frag5_1,
 AVMC(UniMod:4)VAK_1_Frag6_1,
 AYLDELK_2_Frag1_1,
 AYLDELK_2_Frag2_1,
 AYLDELK_2_Frag3_1,
 AYLDELK_2_Frag4_1,
 AYLDELK_2_Frag5_1,
 AYLDELK_2_Frag6_1,
 C(UniMod:4)DLGITGVDQVR_2_Frag1_1,
 C(UniMod:4)DLGITGVDQVR_2_Frag2_1,
 C(UniMod:4)DLGITGVDQVR_2_Frag3_1,
 C(UniMod:4)GALLDPFELINPR_2_Frag1_1,
 C(UniMod:4)GALLDPFELINPR_2_Frag3_1,
 C(UniMod:4)GALLDPFELINPR_2_Frag4_1,
 C(UniMod:4)GALLDPFELINPR_2_Frag5_1,
 DLQENLLVLR_2_Frag2_1,
 DLQENLLVLR_2_Frag3_1,
 DLQENLLVLR_2_Frag6_1
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_DIANNtoMSstatsFormat.R    0 tests    
test_converters_DIANNtoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   13 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   13 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   13 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   13 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   13 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from DIANN imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from DIANN cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using provided annotation.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** Filtering on Global Q Value < 0.01
INFO  [2025-09-29 20:34:59] ** MBR was not used to analyze the data. Now setting names and filtering
INFO  [2025-09-29 20:34:59] -- Filtering on GlobalPGQValue < 0.01
INFO  [2025-09-29 20:34:59] -- Filtering on GlobalQValue < 0.01
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Sequences containing DECOY, Decoys are removed.
INFO  [2025-09-29 20:34:59] ** Sequences containing \(UniMod\:35\) are removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] Proteins with a single feature are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
WARN  [2025-09-29 20:34:59] The following features have missing values in at least one run. MKWVTFISLLFLFSSAYSRG_4_Frag1_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag2_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag3_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag4_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag5_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag6_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag7_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag8_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag9_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag10_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag11_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag12_1
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_DIANNtoMSstatsFormat.R   13 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   14 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   15 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   16 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   18 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   19 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   20 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   21 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   22 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   23 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   24 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   25 tests [0;32mOK[0m 
test_converters_DIANNtoMSstatsFormat.R   26 tests [0;32mOK[0m [0;34m0.3s[0m

test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from DIAUmpire imported successfully.
INFO  [2025-09-29 20:34:59] ** Using selected fragments and peptides.
INFO  [2025-09-29 20:34:59] ** Extracted the data from selected fragments and/or peptides.
INFO  [2025-09-29 20:34:59] ** Raw data from DIAUmpire cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using provided annotation.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, FragmentIon
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_DIAUmpiretoMSstatsFormat.R   13 tests [0;32mOK[0m [0;36m29ms[0m

test_converters_FragPipetoMSstatsFormat.R    0 tests    
test_converters_FragPipetoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from FragPipe imported successfully.
INFO  [2025-09-29 20:34:59] ** Using annotation extracted from quantification data.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_FragPipetoMSstatsFormat.R    0 tests    
test_converters_FragPipetoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_FragPipetoMSstatsFormat.R   13 tests [0;32mOK[0m [0;36m17ms[0m

test_converters_MaxQtoMSstatsFormat.R    0 tests    
test_converters_MaxQtoMSstatsFormat.R    0 tests    
test_converters_MaxQtoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from MaxQuant imported successfully.
INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2025-09-29 20:34:59] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2025-09-29 20:34:59] ** Raw data from MaxQuant cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using provided annotation.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_MaxQtoMSstatsFormat.R    0 tests    
test_converters_MaxQtoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_MaxQtoMSstatsFormat.R   13 tests [0;32mOK[0m [0;36m39ms[0m

test_converters_MetamorpheusToMSstatsFormat.R    0 tests    
test_converters_MetamorpheusToMSstatsFormat.R    0 tests    
test_converters_MetamorpheusToMSstatsFormat.R    0 tests    
test_converters_MetamorpheusToMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from Metamorpheus imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using provided annotation.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_MetamorpheusToMSstatsFormat.R    0 tests    
test_converters_MetamorpheusToMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_MetamorpheusToMSstatsFormat.R   13 tests [0;32mOK[0m [0;36m19ms[0m

test_converters_OpenMStoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from OpenMS imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from OpenMS cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using annotation extracted from quantification data.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_OpenMStoMSstatsFormat.R    0 tests    
test_converters_OpenMStoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_OpenMStoMSstatsFormat.R   13 tests [0;32mOK[0m [0;36m20ms[0m

test_converters_OpenSWATHtoMSstatsFormat.R    0 tests    
test_converters_OpenSWATHtoMSstatsFormat.R    0 tests    
test_converters_OpenSWATHtoMSstatsFormat.R    0 tests    
test_converters_OpenSWATHtoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from OpenSWATH imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from OpenSWATH cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using provided annotation.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Rows with values of decoy equal to 1 are removed 
INFO  [2025-09-29 20:34:59] ** Rows with values not smaller than 0.01 in m_score are removed 
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_OpenSWATHtoMSstatsFormat.R    0 tests    
test_converters_OpenSWATHtoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_OpenSWATHtoMSstatsFormat.R   13 tests [0;32mOK[0m [0;36m24ms[0m

test_converters_PDtoMSstatsFormat.R    0 tests    
test_converters_PDtoMSstatsFormat.R    0 tests    
test_converters_PDtoMSstatsFormat.R    0 tests    
test_converters_PDtoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using provided annotation.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_PDtoMSstatsFormat.R    0 tests    
test_converters_PDtoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_PDtoMSstatsFormat.R   13 tests [0;32mOK[0m [0;36m18ms[0m

test_converters_ProgenesistoMSstatsFormat.R    0 tests    
test_converters_ProgenesistoMSstatsFormat.R    0 tests    
test_converters_ProgenesistoMSstatsFormat.R    0 tests    
test_converters_ProgenesistoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from Progenesis imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from Progenesis cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using provided annotation.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_ProgenesistoMSstatsFormat.R    0 tests    
test_converters_ProgenesistoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_ProgenesistoMSstatsFormat.R   13 tests [0;32mOK[0m [0;36m19ms[0m

test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    
test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    
test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    
test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from ProteinProspector imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from ProteinProspector cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using provided annotation.
INFO  [2025-09-29 20:34:59] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements within each run will be removed.
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-09-29 20:34:59] ** PSMs have been aggregated to peptide ions.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** For peptides overlapped between fractions of Mixture1_1 use the fraction with maximal average abundance.
INFO  [2025-09-29 20:34:59] ** Fractions belonging to same mixture have been combined.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    
test_converters_ProteinProspectortoMSstatsTMTFormat.R    1 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    2 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    3 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    4 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    5 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    6 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    7 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    8 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    9 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   10 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   11 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   12 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   13 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   13 tests [0;32mOK[0m 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   14 tests [0;32mOK[0m [0;36m59ms[0m

test_converters_SkylinetoMSstatsFormat.R    0 tests    
test_converters_SkylinetoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from Skyline imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from Skyline cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using annotation extracted from quantification data.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Rows with values of StandardType equal to iRT are removed 
INFO  [2025-09-29 20:34:59] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN  [2025-09-29 20:34:59] ** DetectionQValue not found in input columns.
INFO  [2025-09-29 20:34:59] ** Sequences containing DECOY, Decoys are removed.
INFO  [2025-09-29 20:34:59] ** Three isotopic preaks per feature and run are summed
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_SkylinetoMSstatsFormat.R    0 tests    
test_converters_SkylinetoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_SkylinetoMSstatsFormat.R   13 tests [0;32mOK[0m [0;36m32ms[0m

test_converters_SpectronauttoMSstatsFormat.R    0 tests    
test_converters_SpectronauttoMSstatsFormat.R    0 tests    INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using annotation extracted from quantification data.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Intensities with values of FExcludedFromQuantification equal to TRUE are replaced with NA
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:34:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_SpectronauttoMSstatsFormat.R    0 tests    
test_converters_SpectronauttoMSstatsFormat.R    1 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R    2 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R    3 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R    4 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R    5 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R    6 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R    7 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R    8 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R    9 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   10 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   11 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   12 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   13 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   13 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   13 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   13 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut imported successfully.

test_converters_SpectronauttoMSstatsFormat.R   14 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   14 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   14 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   14 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut imported successfully.

test_converters_SpectronauttoMSstatsFormat.R   15 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   15 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   15 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   15 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut imported successfully.

test_converters_SpectronauttoMSstatsFormat.R   16 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   16 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   16 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   16 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut imported successfully.

test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut imported successfully.
INFO  [2025-09-29 20:34:59] ** Raw data from Spectronaut cleaned successfully.
INFO  [2025-09-29 20:34:59] ** Using annotation extracted from quantification data.
INFO  [2025-09-29 20:34:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-09-29 20:34:59] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:34:59] ** Intensities with values of FExcludedFromQuantification equal to TRUE are replaced with NA
INFO  [2025-09-29 20:34:59] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Shared peptides are removed.
INFO  [2025-09-29 20:34:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Run annotation merged with quantification data.
INFO  [2025-09-29 20:34:59] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:34:59] ** Fractionation handled.
INFO  [2025-09-29 20:34:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-09-29 20:35:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_SpectronauttoMSstatsFormat.R   17 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   18 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   19 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   20 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   21 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   22 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   23 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   24 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   25 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   26 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   27 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   28 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   29 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   30 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   31 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   32 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   33 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   34 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   35 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   36 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   37 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   38 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   39 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   40 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   41 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   42 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   43 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   44 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   45 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   46 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   47 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   48 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   49 tests [0;32mOK[0m 
test_converters_SpectronauttoMSstatsFormat.R   50 tests [0;32mOK[0m [0;34m0.3s[0m

test_dt.R.....................    0 tests    
test_dt.R.....................    0 tests    
test_dt.R.....................    1 tests [0;32mOK[0m 
test_dt.R.....................    2 tests [0;32mOK[0m 
test_dt.R.....................    3 tests [0;32mOK[0m 
test_dt.R.....................    4 tests [0;32mOK[0m 
test_dt.R.....................    5 tests [0;32mOK[0m 
test_dt.R.....................    6 tests [0;32mOK[0m 
test_dt.R.....................    7 tests [0;32mOK[0m 
test_dt.R.....................    7 tests [0;32mOK[0m 
test_dt.R.....................    8 tests [0;32mOK[0m 
test_dt.R.....................    8 tests [0;32mOK[0m 
test_dt.R.....................    8 tests [0;32mOK[0m 
test_dt.R.....................    9 tests [0;32mOK[0m 
test_dt.R.....................   10 tests [0;32mOK[0m 
test_dt.R.....................   11 tests [0;32mOK[0m [0;36m3ms[0m

test_feature_cleaning.R.......    0 tests    
test_feature_cleaning.R.......    0 tests    
test_feature_cleaning.R.......    0 tests    
test_feature_cleaning.R.......    0 tests    INFO  [2025-09-29 20:35:00] ** Features with one or two measurements across channels within each run are removed.

test_feature_cleaning.R.......    1 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    2 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    3 tests [0;32mOK[0m 
test_feature_cleaning.R.......    3 tests [0;32mOK[0m 
test_feature_cleaning.R.......    3 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Features with all missing measurements across runs are removed.

test_feature_cleaning.R.......    4 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    5 tests [0;32mOK[0m 
test_feature_cleaning.R.......    5 tests [0;32mOK[0m 
test_feature_cleaning.R.......    5 tests [0;32mOK[0m 
test_feature_cleaning.R.......    6 tests [0;32mOK[0m 
test_feature_cleaning.R.......    6 tests [0;32mOK[0m 
test_feature_cleaning.R.......    6 tests [0;32mOK[0m 
test_feature_cleaning.R.......    6 tests [0;32mOK[0m 
test_feature_cleaning.R.......    7 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Three isotopic preaks per feature and run are summed

test_feature_cleaning.R.......    8 tests [0;32mOK[0m 
test_feature_cleaning.R.......    9 tests [0;32mOK[0m 
test_feature_cleaning.R.......    9 tests [0;32mOK[0m 
test_feature_cleaning.R.......    9 tests [0;32mOK[0m 
test_feature_cleaning.R.......    9 tests [0;32mOK[0m 
test_feature_cleaning.R.......    9 tests [0;32mOK[0m 
test_feature_cleaning.R.......    9 tests [0;32mOK[0m 
test_feature_cleaning.R.......    9 tests [0;32mOK[0m 
test_feature_cleaning.R.......    9 tests [0;32mOK[0m 
test_feature_cleaning.R.......    9 tests [0;32mOK[0m 
test_feature_cleaning.R.......   10 tests [0;32mOK[0m 
test_feature_cleaning.R.......   10 tests [0;32mOK[0m 
test_feature_cleaning.R.......   10 tests [0;32mOK[0m 
test_feature_cleaning.R.......   11 tests [0;32mOK[0m 
test_feature_cleaning.R.......   11 tests [0;32mOK[0m 
test_feature_cleaning.R.......   11 tests [0;32mOK[0m 
test_feature_cleaning.R.......   12 tests [0;32mOK[0m 
test_feature_cleaning.R.......   12 tests [0;32mOK[0m 
test_feature_cleaning.R.......   13 tests [0;32mOK[0m 
test_feature_cleaning.R.......   13 tests [0;32mOK[0m 
test_feature_cleaning.R.......   14 tests [0;32mOK[0m 
test_feature_cleaning.R.......   14 tests [0;32mOK[0m 
test_feature_cleaning.R.......   14 tests [0;32mOK[0m 
test_feature_cleaning.R.......   14 tests [0;32mOK[0m 
test_feature_cleaning.R.......   14 tests [0;32mOK[0m 
test_feature_cleaning.R.......   14 tests [0;32mOK[0m 
test_feature_cleaning.R.......   15 tests [0;32mOK[0m 
test_feature_cleaning.R.......   15 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests [0;32mOK[0m 
test_feature_cleaning.R.......   17 tests [0;32mOK[0m 
test_feature_cleaning.R.......   17 tests [0;32mOK[0m 
test_feature_cleaning.R.......   17 tests [0;32mOK[0m 
test_feature_cleaning.R.......   18 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] Proteins with a single feature are removed.

test_feature_cleaning.R.......   19 tests [0;32mOK[0m 
test_feature_cleaning.R.......   20 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:35:00] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......   20 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-09-29 20:35:00] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   20 tests [0;32mOK[0m 
test_feature_cleaning.R.......   21 tests [0;32mOK[0m 
test_feature_cleaning.R.......   22 tests [0;32mOK[0m [0;36m78ms[0m

test_filtering.R..............    0 tests    
test_filtering.R..............    0 tests    
test_filtering.R..............    1 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Sequences containing \+ are removed.

test_filtering.R..............    2 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Sequences containing \+ are removed.

test_filtering.R..............    3 tests [0;32mOK[0m 
test_filtering.R..............    4 tests [0;32mOK[0m 
test_filtering.R..............    5 tests [0;32mOK[0m 
test_filtering.R..............    6 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_1 equal to - are removed 

test_filtering.R..............    7 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_1 equal to +, - are removed 

test_filtering.R..............    8 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_1 equal to + are removed 

test_filtering.R..............    9 tests [0;32mOK[0m 
test_filtering.R..............   10 tests [0;32mOK[0m 
test_filtering.R..............   11 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_1 equal to R are removed 

test_filtering.R..............   12 tests [0;32mOK[0m 
test_filtering.R..............   13 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_2 equal to + are removed 

test_filtering.R..............   14 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_2 equal to X are removed 

test_filtering.R..............   15 tests [0;32mOK[0m 
test_filtering.R..............   16 tests [0;32mOK[0m 
test_filtering.R..............   17 tests [0;32mOK[0m 
test_filtering.R..............   18 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   19 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   20 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   21 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   22 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   23 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   24 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   25 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   26 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Intensities with values not greater than 0.3 in Score are replaced with NA

test_filtering.R..............   26 tests [0;32mOK[0m 
test_filtering.R..............   27 tests [0;32mOK[0m 
test_filtering.R..............   28 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Intensities with values not greater than 0.3 in Score are replaced with NA

test_filtering.R..............   28 tests [0;32mOK[0m 
test_filtering.R..............   29 tests [0;32mOK[0m 
test_filtering.R..............   30 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Intensities with values not smaller than 0.3 in Score are replaced with NA

test_filtering.R..............   30 tests [0;32mOK[0m 
test_filtering.R..............   31 tests [0;32mOK[0m 
test_filtering.R..............   32 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Intensities with values not smaller than 0.3 in Score are replaced with NA

test_filtering.R..............   32 tests [0;32mOK[0m 
test_filtering.R..............   33 tests [0;32mOK[0m 
test_filtering.R..............   34 tests [0;32mOK[0m 
test_filtering.R..............   35 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2025-09-29 20:35:00] ** Sequences containing \+ are removed.

test_filtering.R..............   36 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2025-09-29 20:35:00] ** Sequences containing \+ are removed.

test_filtering.R..............   37 tests [0;32mOK[0m [0;36m12ms[0m

test_fractions.R..............    0 tests    
test_fractions.R..............    1 tests [0;32mOK[0m 
test_fractions.R..............    1 tests [0;32mOK[0m 
test_fractions.R..............    1 tests [0;32mOK[0m 
test_fractions.R..............    1 tests [0;32mOK[0m 
test_fractions.R..............    1 tests [0;32mOK[0m 
test_fractions.R..............    1 tests [0;32mOK[0m 
test_fractions.R..............    2 tests [0;32mOK[0m 
test_fractions.R..............    3 tests [0;32mOK[0m 
test_fractions.R..............    4 tests [0;32mOK[0m 
test_fractions.R..............    4 tests [0;32mOK[0m 
test_fractions.R..............    5 tests [0;32mOK[0m 
test_fractions.R..............    5 tests [0;32mOK[0m 
test_fractions.R..............    5 tests [0;32mOK[0m 
test_fractions.R..............    5 tests [0;32mOK[0m 
test_fractions.R..............    6 tests [0;32mOK[0m 
test_fractions.R..............    7 tests [0;32mOK[0m 
test_fractions.R..............    8 tests [0;32mOK[0m 
test_fractions.R..............    8 tests [0;32mOK[0m INFO  [2025-09-29 20:35:00] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2025-09-29 20:35:00] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2025-09-29 20:35:00] ** For peptides overlapped between fractions of 2_1 use the fraction with maximal average abundance.

test_fractions.R..............    8 tests [0;32mOK[0m 
test_fractions.R..............    9 tests [0;32mOK[0m [0;36m18ms[0m

test_logging.R................    1 tests [0;32mOK[0m 
test_logging.R................    2 tests [0;32mOK[0m 
test_logging.R................    3 tests [0;32mOK[0m [0;36m1ms[0m

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2025-09-29 20:35:00] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2025-09-29 20:35:00] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    1 tests [0;32mOK[0m 
test_shared_peptides.R........    2 tests [0;32mOK[0m 
test_shared_peptides.R........    3 tests [0;32mOK[0m 
test_shared_peptides.R........    4 tests [0;32mOK[0m 
test_shared_peptides.R........    5 tests [0;32mOK[0m [0;36m4ms[0m

test_utils_anomaly_score.R....    0 tests    
test_utils_anomaly_score.R....    0 tests    
test_utils_anomaly_score.R....    0 tests    
test_utils_anomaly_score.R....    0 tests    
test_utils_anomaly_score.R....    0 tests    
test_utils_anomaly_score.R....    1 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    1 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    1 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    2 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    3 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    3 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    3 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    3 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    3 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    4 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    4 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    4 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    4 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    5 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    5 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    5 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    6 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    6 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    6 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    6 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    6 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    6 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    7 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    7 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    7 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    8 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    8 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    8 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    9 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    9 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    9 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    9 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    9 tests [0;32mOK[0m 
test_utils_anomaly_score.R....    9 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   10 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   10 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   11 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   12 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   13 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   14 tests [0;32mOK[0m Top 5 anomalous rows: 20 14 15 8 13 

test_utils_anomaly_score.R....   14 tests [0;32mOK[0m Score range: 0.237877 0.5766361 

test_utils_anomaly_score.R....   14 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   14 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   14 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   15 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   16 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   16 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   16 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   17 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   18 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   19 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   19 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   19 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   19 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   19 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   20 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   21 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   22 tests [0;32mOK[0m All anomaly detection tests completed successfully!

test_utils_anomaly_score.R....   22 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   22 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   22 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   22 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   22 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   22 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   23 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   24 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   24 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   25 tests [0;32mOK[0m 
test_utils_anomaly_score.R....   26 tests [0;32mOK[0m [0;34m2.7s[0m

test_utils_data_health.R......    0 tests    
test_utils_data_health.R......    0 tests    INFO  [2025-09-29 20:35:03] 0% of the values are missing across all intensities

test_utils_data_health.R......    0 tests    
test_utils_data_health.R......    1 tests [0;32mOK[0m 
test_utils_data_health.R......    2 tests [0;32mOK[0m 
test_utils_data_health.R......    2 tests [0;32mOK[0m 
test_utils_data_health.R......    2 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 20% of the values are missing across all intensities

test_utils_data_health.R......    2 tests [0;32mOK[0m 
test_utils_data_health.R......    3 tests [0;32mOK[0m 
test_utils_data_health.R......    3 tests [0;32mOK[0m 
test_utils_data_health.R......    3 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 100% of the values are missing across all intensities

test_utils_data_health.R......    3 tests [0;32mOK[0m 
test_utils_data_health.R......    4 tests [0;32mOK[0m 
test_utils_data_health.R......    4 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] Intensity distribution standard truncated data.

test_utils_data_health.R......    4 tests [0;32mOK[0m 
test_utils_data_health.R......    5 tests [0;32mOK[0m 
test_utils_data_health.R......    5 tests [0;32mOK[0m 
test_utils_data_health.R......    5 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] Intensity distribution indicates zero truncated data. More missing values than normal should be expected.

test_utils_data_health.R......    5 tests [0;32mOK[0m 
test_utils_data_health.R......    6 tests [0;32mOK[0m 
test_utils_data_health.R......    6 tests [0;32mOK[0m 
test_utils_data_health.R......    6 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.

test_utils_data_health.R......    6 tests [0;32mOK[0m 
test_utils_data_health.R......    7 tests [0;32mOK[0m 
test_utils_data_health.R......    8 tests [0;32mOK[0m 
test_utils_data_health.R......    9 tests [0;32mOK[0m 
test_utils_data_health.R......   10 tests [0;32mOK[0m 
test_utils_data_health.R......   11 tests [0;32mOK[0m 
test_utils_data_health.R......   11 tests [0;32mOK[0m 
test_utils_data_health.R......   12 tests [0;32mOK[0m 
test_utils_data_health.R......   13 tests [0;32mOK[0m 
test_utils_data_health.R......   14 tests [0;32mOK[0m 
test_utils_data_health.R......   15 tests [0;32mOK[0m 
test_utils_data_health.R......   15 tests [0;32mOK[0m 
test_utils_data_health.R......   15 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.

test_utils_data_health.R......   15 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 0% of all measured intensities fall within the outlier range

test_utils_data_health.R......   15 tests [0;32mOK[0m 
test_utils_data_health.R......   16 tests [0;32mOK[0m 
test_utils_data_health.R......   17 tests [0;32mOK[0m 
test_utils_data_health.R......   17 tests [0;32mOK[0m 
test_utils_data_health.R......   17 tests [0;32mOK[0m 
test_utils_data_health.R......   18 tests [0;32mOK[0m 
test_utils_data_health.R......   19 tests [0;32mOK[0m 
test_utils_data_health.R......   20 tests [0;32mOK[0m 
test_utils_data_health.R......   21 tests [0;32mOK[0m 
test_utils_data_health.R......   21 tests [0;32mOK[0m 
test_utils_data_health.R......   21 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.

test_utils_data_health.R......   21 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 0% of features are missing in more than half the runs. These features may need to be removed.

test_utils_data_health.R......   21 tests [0;32mOK[0m 
test_utils_data_health.R......   22 tests [0;32mOK[0m 
test_utils_data_health.R......   23 tests [0;32mOK[0m 
test_utils_data_health.R......   24 tests [0;32mOK[0m 
test_utils_data_health.R......   24 tests [0;32mOK[0m 
test_utils_data_health.R......   24 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 20% of features are missing in more than half the runs. These features may need to be removed.

test_utils_data_health.R......   24 tests [0;32mOK[0m 
test_utils_data_health.R......   24 tests [0;32mOK[0m 
test_utils_data_health.R......   24 tests [0;32mOK[0m 
test_utils_data_health.R......   25 tests [0;32mOK[0m 
test_utils_data_health.R......   25 tests [0;32mOK[0m 
test_utils_data_health.R......   25 tests [0;32mOK[0m 
test_utils_data_health.R......   26 tests [0;32mOK[0m 
test_utils_data_health.R......   26 tests [0;32mOK[0m 
test_utils_data_health.R......   26 tests [0;32mOK[0m 
test_utils_data_health.R......   27 tests [0;32mOK[0m 
test_utils_data_health.R......   27 tests [0;32mOK[0m 
test_utils_data_health.R......   27 tests [0;32mOK[0m 
test_utils_data_health.R......   28 tests [0;32mOK[0m 
test_utils_data_health.R......   28 tests [0;32mOK[0m 
test_utils_data_health.R......   28 tests [0;32mOK[0m 
test_utils_data_health.R......   29 tests [0;32mOK[0m 
test_utils_data_health.R......   30 tests [0;32mOK[0m 
test_utils_data_health.R......   31 tests [0;32mOK[0m 
test_utils_data_health.R......   31 tests [0;32mOK[0m 
test_utils_data_health.R......   32 tests [0;32mOK[0m 
test_utils_data_health.R......   33 tests [0;32mOK[0m 
test_utils_data_health.R......   34 tests [0;32mOK[0m 
test_utils_data_health.R......   34 tests [0;32mOK[0m 
test_utils_data_health.R......   35 tests [0;32mOK[0m 
test_utils_data_health.R......   35 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 0% of the values are missing across all intensities
INFO  [2025-09-29 20:35:03] Intensity distribution standard truncated data.
INFO  [2025-09-29 20:35:03] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-09-29 20:35:03] 0% of all measured intensities fall within the outlier range
INFO  [2025-09-29 20:35:03] 0% of features are missing in more than half the runs. These features may need to be removed.

test_utils_data_health.R......   35 tests [0;32mOK[0m 
test_utils_data_health.R......   36 tests [0;32mOK[0m 
test_utils_data_health.R......   37 tests [0;32mOK[0m 
test_utils_data_health.R......   37 tests [0;32mOK[0m 
test_utils_data_health.R......   37 tests [0;32mOK[0m 
test_utils_data_health.R......   38 tests [0;32mOK[0m 
test_utils_data_health.R......   38 tests [0;32mOK[0m 
test_utils_data_health.R......   39 tests [0;32mOK[0m 
test_utils_data_health.R......   40 tests [0;32mOK[0m 
test_utils_data_health.R......   41 tests [0;32mOK[0m 
test_utils_data_health.R......   41 tests [0;32mOK[0m 
test_utils_data_health.R......   42 tests [0;32mOK[0m 
test_utils_data_health.R......   42 tests [0;32mOK[0m 
test_utils_data_health.R......   42 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 0% of the values are missing across all intensities
INFO  [2025-09-29 20:35:03] Intensity distribution standard truncated data.
INFO  [2025-09-29 20:35:03] 0% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-09-29 20:35:03] 0% of all measured intensities fall within the outlier range
INFO  [2025-09-29 20:35:03] 0% of features are missing in more than half the runs. These features may need to be removed.

test_utils_data_health.R......   42 tests [0;32mOK[0m 
test_utils_data_health.R......   43 tests [0;32mOK[0m 
test_utils_data_health.R......   43 tests [0;32mOK[0m 
test_utils_data_health.R......   44 tests [0;32mOK[0m 
test_utils_data_health.R......   44 tests [0;32mOK[0m 
test_utils_data_health.R......   44 tests [0;32mOK[0m 
test_utils_data_health.R......   44 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 0% of the values are missing across all intensities
INFO  [2025-09-29 20:35:03] Intensity distribution standard truncated data.
INFO  [2025-09-29 20:35:03] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-09-29 20:35:03] 0% of all measured intensities fall within the outlier range
INFO  [2025-09-29 20:35:03] 0% of features are missing in more than half the runs. These features may need to be removed.

test_utils_data_health.R......   44 tests [0;32mOK[0m 
test_utils_data_health.R......   44 tests [0;32mOK[0m 
test_utils_data_health.R......   45 tests [0;32mOK[0m 
test_utils_data_health.R......   46 tests [0;32mOK[0m 
test_utils_data_health.R......   46 tests [0;32mOK[0m 
test_utils_data_health.R......   46 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 0% of the values are missing across all intensities
INFO  [2025-09-29 20:35:03] Intensity distribution standard truncated data.
INFO  [2025-09-29 20:35:03] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-09-29 20:35:03] 0% of all measured intensities fall within the outlier range
INFO  [2025-09-29 20:35:03] 0% of features are missing in more than half the runs. These features may need to be removed.

test_utils_data_health.R......   46 tests [0;32mOK[0m 
test_utils_data_health.R......   46 tests [0;32mOK[0m 
test_utils_data_health.R......   47 tests [0;32mOK[0m 
test_utils_data_health.R......   47 tests [0;32mOK[0m 
test_utils_data_health.R......   47 tests [0;32mOK[0m 
test_utils_data_health.R......   47 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] 0% of the values are missing across all intensities
INFO  [2025-09-29 20:35:03] Intensity distribution standard truncated data.
INFO  [2025-09-29 20:35:03] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-09-29 20:35:03] 0% of all measured intensities fall within the outlier range
INFO  [2025-09-29 20:35:03] 0% of features are missing in more than half the runs. These features may need to be removed.

test_utils_data_health.R......   47 tests [0;32mOK[0m 
test_utils_data_health.R......   47 tests [0;32mOK[0m 
test_utils_data_health.R......   48 tests [0;32mOK[0m 
test_utils_data_health.R......   49 tests [0;32mOK[0m [0;36m35ms[0m

test_workflow.R...............    0 tests    
test_workflow.R...............    0 tests    INFO  [2025-09-29 20:35:03] ** Raw data from OpenMS imported successfully.

test_workflow.R...............    0 tests    
test_workflow.R...............    1 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] ** Raw data from OpenMS cleaned successfully.

test_workflow.R...............    1 tests [0;32mOK[0m 
test_workflow.R...............    2 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] ** Using annotation extracted from quantification data.
INFO  [2025-09-29 20:35:03] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_workflow.R...............    2 tests [0;32mOK[0m 
test_workflow.R...............    3 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-09-29 20:35:03] ** Features with all missing measurements across runs are removed.
INFO  [2025-09-29 20:35:03] ** Shared peptides are removed.
INFO  [2025-09-29 20:35:03] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-09-29 20:35:03] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:35:03] Proteins with a single feature are removed.
INFO  [2025-09-29 20:35:03] ** Run annotation merged with quantification data.

test_workflow.R...............    3 tests [0;32mOK[0m 
test_workflow.R...............    4 tests [0;32mOK[0m 
test_workflow.R...............    5 tests [0;32mOK[0m 
test_workflow.R...............    6 tests [0;32mOK[0m INFO  [2025-09-29 20:35:03] ** Features with one or two measurements across runs are removed.
INFO  [2025-09-29 20:35:03] ** Fractionation handled.
INFO  [2025-09-29 20:35:03] ** Updated quantification data to make balanced design. Missing values are marked by NA

test_workflow.R...............    6 tests [0;32mOK[0m 
test_workflow.R...............    7 tests [0;32mOK[0m 
test_workflow.R...............    8 tests [0;32mOK[0m [0;36m25ms[0m
All ok, 497 results (4.2s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> 
> proc.time()
   user  system elapsed 
  1.374   0.159   4.401

Example timings

MSstatsConvert.Rcheck/MSstatsConvert-Ex.timings

name	user	system	elapsed
DIANNtoMSstatsFormat	0.274	0.022	0.298
DIAUmpiretoMSstatsFormat	0.028	0.002	0.031
FragPipetoMSstatsFormat	0.018	0.002	0.019
MSstatsBalancedDesign	0.006	0.000	0.006
MSstatsClean	0.046	0.003	0.051
MSstatsImport	0.044	0.003	0.048
MSstatsLogsSettings	0.003	0.001	0.004
MSstatsMakeAnnotation	0.058	0.003	0.062
MSstatsPreprocess	0.055	0.004	0.058
MSstatsSaveSessionInfo	0.005	0.002	0.009
MaxQtoMSstatsFormat	0.030	0.006	0.042
MetamorpheusToMSstatsFormat	0.017	0.001	0.019
OpenMStoMSstatsFormat	0.019	0.000	0.019
OpenSWATHtoMSstatsFormat	0.018	0.001	0.019
PDtoMSstatsFormat	0.020	0.001	0.027
ProgenesistoMSstatsFormat	0.019	0.001	0.021
ProteinProspectortoMSstatsTMTFormat	0.073	0.002	0.075
SkylinetoMSstatsFormat	0.028	0.002	0.030
SpectronauttoMSstatsFormat	0.016	0.001	0.018
getDataType	0.041	0.001	0.043
getInputFile	0.042	0.002	0.044