Back to Multiple platform build/check report for BioC 3.23:   simplified   long
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This page was generated on 2026-04-13 11:35 -0400 (Mon, 13 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 alpha (2026-04-05 r89794) 4919
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-04-08 r89818) 4632
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

Package 1417/2390HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsConvert 1.21.2  (landing page)
Anthony Wu
Snapshot Date: 2026-04-12 13:40 -0400 (Sun, 12 Apr 2026)
git_url: https://git.bioconductor.org/packages/MSstatsConvert
git_branch: devel
git_last_commit: ffcbd23
git_last_commit_date: 2026-04-10 15:33:26 -0400 (Fri, 10 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
See other builds for MSstatsConvert in R Universe.

CHECK results for MSstatsConvert on nebbiolo1

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: 1.21.2
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSstatsConvert_1.21.2.tar.gz
StartedAt: 2026-04-13 02:53:42 -0400 (Mon, 13 Apr 2026)
EndedAt: 2026-04-13 02:54:37 -0400 (Mon, 13 Apr 2026)
EllapsedTime: 55.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsConvert.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSstatsConvert_1.21.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MSstatsConvert.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-13 06:53:42 UTC
* checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK
* this is package ‘MSstatsConvert’ version ‘1.21.2’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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
.addSpectronautColumnsIfMissing: no visible binding for global variable
  ‘FFrgLossType’
.addSpectronautColumnsIfMissing: no visible binding for global variable
  ‘FExcludedFromQuantification’
.addSpectronautColumnsIfMissing: no visible binding for global variable
  ‘FFrgIon’
.addSpectronautColumnsIfMissing: no visible binding for global variable
  ‘FCharge’
.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’
.cleanDIANNCleanAndFilterData: no visible binding for global variable
  ‘QValue’
.cleanDIANNCleanAndFilterData: no visible binding for global variable
  ‘LibPGQValue’
.cleanDIANNCleanAndFilterData: no visible binding for global variable
  ‘LibQValue’
.cleanDIANNCleanAndFilterData: no visible binding for global variable
  ‘GlobalPGQValue’
.cleanDIANNCleanAndFilterData: no visible binding for global variable
  ‘GlobalQValue’
.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’
.removeOverlappingFeatures: no visible binding for global variable
  ‘IsotopeLabelType’
.removeOverlappingFeatures: no visible binding for global variable
  ‘Intensity’
.removeOverlappingFeatures: no visible global function definition for
  ‘.’
.removeOverlappingFeatures: no visible binding for global variable
  ‘Run’
.removeOverlappingFeatures: no visible binding for global variable
  ‘feature’
.removeOverlappingFeatures: no visible binding for global variable
  ‘is_max’
.removeOverlappingFeatures: no visible binding for global variable
  ‘n_obs’
.resolveFractionTies: no visible global function definition for ‘.’
.resolveFractionTies: no visible binding for global variable ‘n_ties’
.resolveFractionTies: no visible binding for global variable ‘feature’
.resolveFractionTies: no visible binding for global variable ‘Fraction’
.resolveFractionTies: no visible binding for global variable
  ‘IsotopeLabelType’
.resolveFractionTies: no visible binding for global variable
  ‘Intensity’
.resolveFractionTies: no visible binding for global variable
  ‘mean_abundance’
.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
  ‘Intensity’
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 FCharge
  FExcludedFromQuantification FFrgIon FFrgLossType Feature Fraction
  Fragment FragmentInfo FragmentIon FragmentQuantCorrected
  GlobalPGQValue GlobalQValue Intensity IsotopeLabelType LibPGQValue
  LibQValue MeanAbundance Order PSM PeptideProphet.Probability
  PeptideSequence PrecursorMz ProductCharge ProteinName Purity QValue
  Run count feature feature_rank is_max is_outlier mean_Intensity
  mean_abundance modifyList n_obs n_ties 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 ... INFO
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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/MSstatsConvert.Rcheck/00check.log’
for details.

Installation output

MSstatsConvert.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MSstatsConvert
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘MSstatsConvert’ ...
** this is package ‘MSstatsConvert’ version ‘1.21.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c isolation_forest.cpp -o isolation_forest.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o MSstatsConvert.so RcppExports.o isolation_forest.o -fopenmp -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 OK 
test_MSstatsConvert.R.........    2 tests OK 
test_MSstatsConvert.R.........    3 tests OK 
test_MSstatsConvert.R.........    4 tests OK 
test_MSstatsConvert.R.........    5 tests OK 
test_MSstatsConvert.R.........    6 tests OK 64ms

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  [2026-04-13 02:54:13] ** Using annotation extracted from quantification data.
INFO  [2026-04-13 02:54:13] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    1 tests OK INFO  [2026-04-13 02:54:13] ** Using provided annotation.
INFO  [2026-04-13 02:54:13] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    2 tests OK 
test_annotation.R.............    2 tests OK INFO  [2026-04-13 02:54:13] ** Using provided annotation.
INFO  [2026-04-13 02:54:13] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    3 tests OK INFO  [2026-04-13 02:54:13] ** Using provided annotation.
INFO  [2026-04-13 02:54:13] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    4 tests OK 
test_annotation.R.............    4 tests OK 
test_annotation.R.............    4 tests OK 
test_annotation.R.............    5 tests OK INFO  [2026-04-13 02:54:13] ** Run annotation merged with quantification data.

test_annotation.R.............    6 tests OK INFO  [2026-04-13 02:54:13] ** Using provided annotation.
INFO  [2026-04-13 02:54:13] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    6 tests OK INFO  [2026-04-13 02:54:13] ** Run annotation merged with quantification data.

test_annotation.R.............    7 tests OK INFO  [2026-04-13 02:54:13] ** Using provided annotation.
INFO  [2026-04-13 02:54:13] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    7 tests OK 
test_annotation.R.............    8 tests OK INFO  [2026-04-13 02:54:13] ** Using provided annotation.
INFO  [2026-04-13 02:54:13] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    8 tests OK 
test_annotation.R.............    9 tests OK 
test_annotation.R.............   10 tests OK INFO  [2026-04-13 02:54:13] ** Using provided annotation.

test_annotation.R.............   11 tests OK 68ms

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 OK 
test_balanced_design.R........    2 tests OK 
test_balanced_design.R........    3 tests OK 
test_balanced_design.R........    3 tests OK 
test_balanced_design.R........    3 tests OK 
test_balanced_design.R........    3 tests OK 
test_balanced_design.R........    4 tests OK 
test_balanced_design.R........    4 tests OK 
test_balanced_design.R........    4 tests OK 
test_balanced_design.R........    4 tests OK 
test_balanced_design.R........    4 tests OK 
test_balanced_design.R........    4 tests OK 
test_balanced_design.R........    4 tests OK 
test_balanced_design.R........    5 tests OK 
test_balanced_design.R........    5 tests OK 
test_balanced_design.R........    6 tests OK 
test_balanced_design.R........    7 tests OK 
test_balanced_design.R........    7 tests OK 
test_balanced_design.R........    7 tests OK 
test_balanced_design.R........    7 tests OK 
test_balanced_design.R........    7 tests OK 
test_balanced_design.R........    7 tests OK 
test_balanced_design.R........    7 tests OK 
test_balanced_design.R........    7 tests OK 
test_balanced_design.R........    8 tests OK 
test_balanced_design.R........    9 tests OK 
test_balanced_design.R........   10 tests OK 
test_balanced_design.R........   11 tests OK 
test_balanced_design.R........   11 tests OK 
test_balanced_design.R........   11 tests OK 
test_balanced_design.R........   11 tests OK 
test_balanced_design.R........   12 tests OK 
test_balanced_design.R........   13 tests OK 
test_balanced_design.R........   13 tests OK 
test_balanced_design.R........   14 tests OK 
test_balanced_design.R........   15 tests OK 
test_balanced_design.R........   15 tests OK 
test_balanced_design.R........   15 tests OK 
test_balanced_design.R........   16 tests OK 
test_balanced_design.R........   17 tests OK 
test_balanced_design.R........   17 tests OK 
test_balanced_design.R........   17 tests OK 
test_balanced_design.R........   17 tests OK 
test_balanced_design.R........   18 tests OK 
test_balanced_design.R........   18 tests OK 
test_balanced_design.R........   19 tests OK 
test_balanced_design.R........   20 tests OK 
test_balanced_design.R........   21 tests OK 91ms

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2026-04-13 02:54:13] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2026-04-13 02:54:13] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2026-04-13 02:54:13] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2026-04-13 02:54:13] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2026-04-13 02:54:13] ** Using selected fragments and peptides.
INFO  [2026-04-13 02:54:13] ** Extracted the data from selected fragments and/or peptides.
INFO  [2026-04-13 02:54:13] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2026-04-13 02:54:13] ** Using selected fragments and peptides.
INFO  [2026-04-13 02:54:13] ** Extracted the data from selected fragments and/or peptides.
INFO  [2026-04-13 02:54:13] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2026-04-13 02:54:13] ** Using selected fragments.
INFO  [2026-04-13 02:54:13] ** Extracted the data from selected fragments and/or peptides.
INFO  [2026-04-13 02:54:13] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    1 tests OK 
test_cleanRaw.R...............    2 tests OK 
test_cleanRaw.R...............    3 tests OK 
test_cleanRaw.R...............    4 tests OK 
test_cleanRaw.R...............    5 tests OK 
test_cleanRaw.R...............    6 tests OK 
test_cleanRaw.R...............    7 tests OK 
test_cleanRaw.R...............    8 tests OK 
test_cleanRaw.R...............    9 tests OK 
test_cleanRaw.R...............    9 tests OK 
test_cleanRaw.R...............    9 tests OK INFO  [2026-04-13 02:54:13] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2026-04-13 02:54:13] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:13] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:13] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:13] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:13] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2026-04-13 02:54:13] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2026-04-13 02:54:14] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2026-04-13 02:54:14] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2026-04-13 02:54:14] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests OK 
test_cleanRaw.R...............   10 tests OK 
test_cleanRaw.R...............   11 tests OK INFO  [2026-04-13 02:54:14] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:14] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2026-04-13 02:54:14] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............   12 tests OK 
test_cleanRaw.R...............   13 tests OK 
test_cleanRaw.R...............   13 tests OK 
test_cleanRaw.R...............   13 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............   13 tests OK INFO  [2026-04-13 02:54:14] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:14] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:14] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2026-04-13 02:54:14] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:14] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............   13 tests OK 
test_cleanRaw.R...............   14 tests OK 
test_cleanRaw.R...............   15 tests OK 
test_cleanRaw.R...............   15 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   15 tests OK 
test_cleanRaw.R...............   16 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   17 tests OK 
test_cleanRaw.R...............   18 tests OK 
test_cleanRaw.R...............   18 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   18 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   18 tests OK 
test_cleanRaw.R...............   19 tests OK 
test_cleanRaw.R...............   20 tests OK 
test_cleanRaw.R...............   20 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from OpenSWATH imported successfully.

test_cleanRaw.R...............   20 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from OpenSWATH cleaned successfully.

test_cleanRaw.R...............   20 tests OK 
test_cleanRaw.R...............   21 tests OK 
test_cleanRaw.R...............   22 tests OK 
test_cleanRaw.R...............   22 tests OK 
test_cleanRaw.R...............   22 tests OK 
test_cleanRaw.R...............   22 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests OK 
test_cleanRaw.R...............   23 tests OK 
test_cleanRaw.R...............   24 tests OK 
test_cleanRaw.R...............   25 tests OK 
test_cleanRaw.R...............   25 tests OK 
test_cleanRaw.R...............   25 tests OK 
test_cleanRaw.R...............   25 tests OK 
test_cleanRaw.R...............   25 tests OK 
test_cleanRaw.R...............   25 tests OK 
test_cleanRaw.R...............   25 tests OK 
test_cleanRaw.R...............   25 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK 
test_cleanRaw.R...............   26 tests OK 
test_cleanRaw.R...............   27 tests OK 
test_cleanRaw.R...............   28 tests OK 
test_cleanRaw.R...............   29 tests OK 
test_cleanRaw.R...............   30 tests OK 
test_cleanRaw.R...............   30 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK 
test_cleanRaw.R...............   30 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests OK 
test_cleanRaw.R...............   31 tests OK 
test_cleanRaw.R...............   32 tests OK 
test_cleanRaw.R...............   33 tests OK 
test_cleanRaw.R...............   33 tests OK 
test_cleanRaw.R...............   33 tests OK 
test_cleanRaw.R...............   33 tests OK 
test_cleanRaw.R...............   33 tests OK 
test_cleanRaw.R...............   33 tests OK 
test_cleanRaw.R...............   33 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests OK 
test_cleanRaw.R...............   34 tests OK 
test_cleanRaw.R...............   35 tests OK 
test_cleanRaw.R...............   36 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   37 tests OK 
test_cleanRaw.R...............   37 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from SpectroMine cleaned successfully.

test_cleanRaw.R...............   37 tests OK 
test_cleanRaw.R...............   38 tests OK 
test_cleanRaw.R...............   39 tests OK ERROR [2026-04-13 02:54:14] There is no channel intensity column in the input data, which should start with 'PSM' and end with 'Raw'.

test_cleanRaw.R...............   40 tests OK 
test_cleanRaw.R...............   40 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Spectronaut cleaned successfully.

test_cleanRaw.R...............   40 tests OK 
test_cleanRaw.R...............   41 tests OK 
test_cleanRaw.R...............   42 tests OK 
test_cleanRaw.R...............   42 tests OK 
test_cleanRaw.R...............   42 tests OK 
test_cleanRaw.R...............   42 tests OK 
test_cleanRaw.R...............   42 tests OK 
test_cleanRaw.R...............   42 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   42 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Spectronaut cleaned successfully.

test_cleanRaw.R...............   42 tests OK 
test_cleanRaw.R...............   43 tests OK 
test_cleanRaw.R...............   44 tests OK 
test_cleanRaw.R...............   44 tests OK INFO  [2026-04-13 02:54:14] ** Raw data from Metamorpheus imported successfully.

test_cleanRaw.R...............   44 tests OK 
test_cleanRaw.R...............   45 tests OK 0.7s

test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............    0 tests    INFO  [2026-04-13 02:54:14] ** Filtering on Q.Value < 0.01
INFO  [2026-04-13 02:54:14] ** MBR was used to analyze the data. Now setting names and filtering
INFO  [2026-04-13 02:54:14] -- LibPGQValue < 0.01
INFO  [2026-04-13 02:54:14] -- LibQValue < 0.01
INFO  [2026-04-13 02:54:14] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............   15 tests OK INFO  [2026-04-13 02:54:14] ** Filtering on Q.Value < 0.01
INFO  [2026-04-13 02:54:14] ** MBR was used to analyze the data. Now setting names and filtering
INFO  [2026-04-13 02:54:14] -- LibPGQValue < 0.01
INFO  [2026-04-13 02:54:14] -- LibQValue < 0.01
INFO  [2026-04-13 02:54:14] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............   15 tests OK 
test_clean_DIANN.R............   30 tests OK 
test_clean_DIANN.R............   30 tests OK INFO  [2026-04-13 02:54:14] ** Filtering on Q.Value < 0.005
INFO  [2026-04-13 02:54:14] ** MBR was used to analyze the data. Now setting names and filtering
INFO  [2026-04-13 02:54:14] -- LibPGQValue < 0.01
INFO  [2026-04-13 02:54:14] -- LibQValue < 0.01
INFO  [2026-04-13 02:54:14] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............   30 tests OK 
test_clean_DIANN.R............   32 tests OK INFO  [2026-04-13 02:54:14] ** Filtering on Q.Value < 0.01
INFO  [2026-04-13 02:54:14] ** MBR was used to analyze the data. Now setting names and filtering
INFO  [2026-04-13 02:54:14] -- LibPGQValue < 0.01
INFO  [2026-04-13 02:54:14] -- LibQValue < 1e-05
INFO  [2026-04-13 02:54:14] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............   32 tests OK 
test_clean_DIANN.R............   34 tests OK INFO  [2026-04-13 02:54:14] ** Filtering on Q.Value < 0.01
INFO  [2026-04-13 02:54:14] ** MBR was used to analyze the data. Now setting names and filtering
INFO  [2026-04-13 02:54:14] -- LibPGQValue < 0.001
INFO  [2026-04-13 02:54:14] -- LibQValue < 0.01
INFO  [2026-04-13 02:54:14] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............   34 tests OK 
test_clean_DIANN.R............   36 tests OK INFO  [2026-04-13 02:54:14] ** Filtering on Q.Value < 0.01
INFO  [2026-04-13 02:54:14] ** MBR was not used to analyze the data. Now setting names and filtering
INFO  [2026-04-13 02:54:14] -- Filtering on GlobalPGQValue < 0.01
INFO  [2026-04-13 02:54:14] -- Filtering on GlobalQValue < 0.001
INFO  [2026-04-13 02:54:14] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............   36 tests OK 
test_clean_DIANN.R............   38 tests OK INFO  [2026-04-13 02:54:14] ** Filtering on Q.Value < 0.01
INFO  [2026-04-13 02:54:14] ** MBR was not used to analyze the data. Now setting names and filtering
INFO  [2026-04-13 02:54:14] -- Filtering on GlobalPGQValue < 2e-04
INFO  [2026-04-13 02:54:14] -- Filtering on GlobalQValue < 0.01
INFO  [2026-04-13 02:54:14] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............   38 tests OK 
test_clean_DIANN.R............   40 tests OK 0.1s

test_clean_Metamorpheus.R.....    0 tests    
test_clean_Metamorpheus.R.....    0 tests    INFO  [2026-04-13 02:54:14] ** Raw data from Metamorpheus cleaned successfully.

test_clean_Metamorpheus.R.....    0 tests    
test_clean_Metamorpheus.R.....    1 tests OK 
test_clean_Metamorpheus.R.....    2 tests OK 
test_clean_Metamorpheus.R.....    3 tests OK 
test_clean_Metamorpheus.R.....    4 tests OK 
test_clean_Metamorpheus.R.....    5 tests OK 
test_clean_Metamorpheus.R.....    6 tests OK 
test_clean_Metamorpheus.R.....    7 tests OK 7ms

test_clean_ProteinProspector.R    0 tests    
test_clean_ProteinProspector.R    0 tests    
test_clean_ProteinProspector.R    0 tests    INFO  [2026-04-13 02:54:14] ** Raw data from ProteinProspector cleaned successfully.

test_clean_ProteinProspector.R    3 tests OK 8ms

test_clean_ProteomeDiscoverer.R    0 tests    
test_clean_ProteomeDiscoverer.R    0 tests    
test_clean_ProteomeDiscoverer.R    0 tests    
test_clean_ProteomeDiscoverer.R    3 tests OK 
test_clean_ProteomeDiscoverer.R    3 tests OK 
test_clean_ProteomeDiscoverer.R    3 tests OK 
test_clean_ProteomeDiscoverer.R    4 tests OK 
test_clean_ProteomeDiscoverer.R    4 tests OK 
test_clean_ProteomeDiscoverer.R    4 tests OK 
test_clean_ProteomeDiscoverer.R    7 tests OK 0.2s

test_clean_Spectronaut.R......    0 tests    
test_clean_Spectronaut.R......    0 tests    
test_clean_Spectronaut.R......    0 tests    INFO  [2026-04-13 02:54:14] ** Raw data from Spectronaut imported successfully.

test_clean_Spectronaut.R......    0 tests    INFO  [2026-04-13 02:54:14] ** Raw data from Spectronaut cleaned successfully.

test_clean_Spectronaut.R......    0 tests    
test_clean_Spectronaut.R......    1 tests OK 
test_clean_Spectronaut.R......    2 tests OK 
test_clean_Spectronaut.R......    2 tests OK 
test_clean_Spectronaut.R......    2 tests OK 
test_clean_Spectronaut.R......    2 tests OK 
test_clean_Spectronaut.R......    3 tests OK 
test_clean_Spectronaut.R......    4 tests OK 
test_clean_Spectronaut.R......    4 tests OK 
test_clean_Spectronaut.R......    4 tests OK 
test_clean_Spectronaut.R......    5 tests OK 
test_clean_Spectronaut.R......    6 tests OK 
test_clean_Spectronaut.R......    6 tests OK 
test_clean_Spectronaut.R......    6 tests OK 
test_clean_Spectronaut.R......    7 tests OK 25ms

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  [2026-04-13 02:54:14] ** Raw data from DIANN imported successfully.
INFO  [2026-04-13 02:54:14] ** Filtering on Q.Value < 0.01
INFO  [2026-04-13 02:54:14] ** MBR was not used to analyze the data. Now setting names and filtering
INFO  [2026-04-13 02:54:14] -- Filtering on GlobalPGQValue < 0.01
INFO  [2026-04-13 02:54:14] -- Filtering on GlobalQValue < 0.01
INFO  [2026-04-13 02:54:14] ** Raw data from DIANN cleaned successfully.
INFO  [2026-04-13 02:54:14] ** Using provided annotation.
INFO  [2026-04-13 02:54:14] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:14] ** 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  [2026-04-13 02:54:14] ** Sequences containing DECOY, Decoys are removed.
INFO  [2026-04-13 02:54:14] ** Sequences containing \(UniMod\:35\) are removed.
INFO  [2026-04-13 02:54:14] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:14] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:14] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:14] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:14] Proteins with a single feature are removed.
INFO  [2026-04-13 02:54:14] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:14] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:14] ** 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 OK 
test_converters_DIANNtoMSstatsFormat.R    2 tests OK 
test_converters_DIANNtoMSstatsFormat.R    3 tests OK 
test_converters_DIANNtoMSstatsFormat.R    4 tests OK 
test_converters_DIANNtoMSstatsFormat.R    5 tests OK 
test_converters_DIANNtoMSstatsFormat.R    6 tests OK 
test_converters_DIANNtoMSstatsFormat.R    7 tests OK 
test_converters_DIANNtoMSstatsFormat.R    8 tests OK 
test_converters_DIANNtoMSstatsFormat.R    9 tests OK 
test_converters_DIANNtoMSstatsFormat.R   10 tests OK 
test_converters_DIANNtoMSstatsFormat.R   11 tests OK 
test_converters_DIANNtoMSstatsFormat.R   12 tests OK 
test_converters_DIANNtoMSstatsFormat.R   13 tests OK 
test_converters_DIANNtoMSstatsFormat.R   13 tests OK 
test_converters_DIANNtoMSstatsFormat.R   13 tests OK 
test_converters_DIANNtoMSstatsFormat.R   13 tests OK 
test_converters_DIANNtoMSstatsFormat.R   13 tests OK INFO  [2026-04-13 02:54:15] ** Raw data from DIANN imported successfully.
INFO  [2026-04-13 02:54:15] ** Filtering on Q.Value < 0.01
INFO  [2026-04-13 02:54:15] ** MBR was not used to analyze the data. Now setting names and filtering
INFO  [2026-04-13 02:54:15] -- Filtering on GlobalPGQValue < 0.01
INFO  [2026-04-13 02:54:15] -- Filtering on GlobalQValue < 0.01
INFO  [2026-04-13 02:54:15] ** Raw data from DIANN cleaned successfully.
INFO  [2026-04-13 02:54:15] ** Using provided annotation.
INFO  [2026-04-13 02:54:15] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:15] ** 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  [2026-04-13 02:54:15] ** Sequences containing DECOY, Decoys are removed.
INFO  [2026-04-13 02:54:15] ** Sequences containing \(UniMod\:35\) are removed.
INFO  [2026-04-13 02:54:15] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:15] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:15] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:15] Proteins with a single feature are removed.
INFO  [2026-04-13 02:54:15] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:15] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:15] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_DIANNtoMSstatsFormat.R   13 tests OK 
test_converters_DIANNtoMSstatsFormat.R   14 tests OK 
test_converters_DIANNtoMSstatsFormat.R   15 tests OK 
test_converters_DIANNtoMSstatsFormat.R   16 tests OK 
test_converters_DIANNtoMSstatsFormat.R   17 tests OK 
test_converters_DIANNtoMSstatsFormat.R   18 tests OK 
test_converters_DIANNtoMSstatsFormat.R   19 tests OK 
test_converters_DIANNtoMSstatsFormat.R   20 tests OK 
test_converters_DIANNtoMSstatsFormat.R   21 tests OK 
test_converters_DIANNtoMSstatsFormat.R   22 tests OK 
test_converters_DIANNtoMSstatsFormat.R   23 tests OK 
test_converters_DIANNtoMSstatsFormat.R   24 tests OK 
test_converters_DIANNtoMSstatsFormat.R   25 tests OK 
test_converters_DIANNtoMSstatsFormat.R   26 tests OK 0.8s

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  [2026-04-13 02:54:15] ** Raw data from DIAUmpire imported successfully.
INFO  [2026-04-13 02:54:15] ** Using selected fragments and peptides.
INFO  [2026-04-13 02:54:15] ** Extracted the data from selected fragments and/or peptides.
INFO  [2026-04-13 02:54:15] ** Raw data from DIAUmpire cleaned successfully.
INFO  [2026-04-13 02:54:15] ** Using provided annotation.
INFO  [2026-04-13 02:54:15] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:15] ** 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  [2026-04-13 02:54:15] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:15] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:15] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:15] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Fractionation handled.
INFO  [2026-04-13 02:54:15] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:15] ** 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 OK 
test_converters_DIAUmpiretoMSstatsFormat.R    2 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R    3 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R    4 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R    5 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R    6 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R    7 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R    8 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R    9 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R   10 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R   11 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R   12 tests OK 
test_converters_DIAUmpiretoMSstatsFormat.R   13 tests OK 98ms

test_converters_FragPipetoMSstatsFormat.R    0 tests    
test_converters_FragPipetoMSstatsFormat.R    0 tests    INFO  [2026-04-13 02:54:15] ** Raw data from FragPipe imported successfully.
INFO  [2026-04-13 02:54:15] ** Using annotation extracted from quantification data.
INFO  [2026-04-13 02:54:15] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:15] ** 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  [2026-04-13 02:54:15] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:15] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:15] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:15] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Fractionation handled.
INFO  [2026-04-13 02:54:15] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:15] ** 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 OK 
test_converters_FragPipetoMSstatsFormat.R    2 tests OK 
test_converters_FragPipetoMSstatsFormat.R    3 tests OK 
test_converters_FragPipetoMSstatsFormat.R    4 tests OK 
test_converters_FragPipetoMSstatsFormat.R    5 tests OK 
test_converters_FragPipetoMSstatsFormat.R    6 tests OK 
test_converters_FragPipetoMSstatsFormat.R    7 tests OK 
test_converters_FragPipetoMSstatsFormat.R    8 tests OK 
test_converters_FragPipetoMSstatsFormat.R    9 tests OK 
test_converters_FragPipetoMSstatsFormat.R   10 tests OK 
test_converters_FragPipetoMSstatsFormat.R   11 tests OK 
test_converters_FragPipetoMSstatsFormat.R   12 tests OK 
test_converters_FragPipetoMSstatsFormat.R   13 tests OK 63ms

test_converters_MaxQtoMSstatsFormat.R    0 tests    
test_converters_MaxQtoMSstatsFormat.R    0 tests    
test_converters_MaxQtoMSstatsFormat.R    0 tests    INFO  [2026-04-13 02:54:15] ** Raw data from MaxQuant imported successfully.
INFO  [2026-04-13 02:54:15] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:15] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:15] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:15] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:15] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2026-04-13 02:54:15] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2026-04-13 02:54:15] ** Raw data from MaxQuant cleaned successfully.
INFO  [2026-04-13 02:54:15] ** Using provided annotation.
INFO  [2026-04-13 02:54:15] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:15] ** 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  [2026-04-13 02:54:15] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:15] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:15] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:15] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:15] ** Fractionation handled.
INFO  [2026-04-13 02:54:15] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:15] ** 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 OK 
test_converters_MaxQtoMSstatsFormat.R    2 tests OK 
test_converters_MaxQtoMSstatsFormat.R    3 tests OK 
test_converters_MaxQtoMSstatsFormat.R    4 tests OK 
test_converters_MaxQtoMSstatsFormat.R    5 tests OK 
test_converters_MaxQtoMSstatsFormat.R    6 tests OK 
test_converters_MaxQtoMSstatsFormat.R    7 tests OK 
test_converters_MaxQtoMSstatsFormat.R    8 tests OK 
test_converters_MaxQtoMSstatsFormat.R    9 tests OK 
test_converters_MaxQtoMSstatsFormat.R   10 tests OK 
test_converters_MaxQtoMSstatsFormat.R   11 tests OK 
test_converters_MaxQtoMSstatsFormat.R   12 tests OK 
test_converters_MaxQtoMSstatsFormat.R   13 tests OK 0.1s

test_converters_MaxQtoMSstatsTMTFormat.R    0 tests    
test_converters_MaxQtoMSstatsTMTFormat.R    0 tests    
test_converters_MaxQtoMSstatsTMTFormat.R    0 tests    INFO  [2026-04-13 02:54:15] ** Raw data from MaxQuant imported successfully.
INFO  [2026-04-13 02:54:15] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:15] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:15] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:15] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:15] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2026-04-13 02:54:15] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:15] ** Raw data from MaxQuant cleaned successfully.
INFO  [2026-04-13 02:54:15] ** Using provided annotation.
INFO  [2026-04-13 02:54:15] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:15] ** 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  [2026-04-13 02:54:15] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:15] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:15] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:15] ** PSMs have been aggregated to peptide ions.
INFO  [2026-04-13 02:54:15] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:15] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:15] ** Fractionation handled.
INFO  [2026-04-13 02:54:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:16] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_converters_MaxQtoMSstatsTMTFormat.R    0 tests    
test_converters_MaxQtoMSstatsTMTFormat.R    1 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R    2 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R    3 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R    4 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R    5 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R    6 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R    7 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R    8 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R    9 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R   10 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R   11 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R   12 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R   13 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R   13 tests OK INFO  [2026-04-13 02:54:16] ** Raw data from MaxQuant imported successfully.
INFO  [2026-04-13 02:54:16] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:16] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:16] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2026-04-13 02:54:16] ** Rows with values of Reverse equal to + are removed 
INFO  [2026-04-13 02:54:16] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2026-04-13 02:54:16] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** Raw data from MaxQuant cleaned successfully.
INFO  [2026-04-13 02:54:16] ** Using provided annotation.
INFO  [2026-04-13 02:54:16] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:16] ** 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  [2026-04-13 02:54:16] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** PSMs have been aggregated to peptide ions.

test_converters_MaxQtoMSstatsTMTFormat.R   14 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R   14 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R   14 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R   14 tests OK 
test_converters_MaxQtoMSstatsTMTFormat.R   15 tests OK 0.3s

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  [2026-04-13 02:54:16] ** Raw data from Metamorpheus imported successfully.
INFO  [2026-04-13 02:54:16] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2026-04-13 02:54:16] ** Using provided annotation.
INFO  [2026-04-13 02:54:16] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:16] ** 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  [2026-04-13 02:54:16] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:16] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Fractionation handled.
INFO  [2026-04-13 02:54:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:16] ** 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 OK 
test_converters_MetamorpheusToMSstatsFormat.R    2 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R    3 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R    4 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R    5 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R    6 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R    7 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R    8 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R    9 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R   10 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R   11 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R   12 tests OK 
test_converters_MetamorpheusToMSstatsFormat.R   13 tests OK 62ms

test_converters_OpenMStoMSstatsFormat.R    0 tests    INFO  [2026-04-13 02:54:16] ** Raw data from OpenMS imported successfully.
INFO  [2026-04-13 02:54:16] ** Raw data from OpenMS cleaned successfully.
INFO  [2026-04-13 02:54:16] ** Using annotation extracted from quantification data.
INFO  [2026-04-13 02:54:16] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:16] ** 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  [2026-04-13 02:54:16] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:16] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Fractionation handled.
INFO  [2026-04-13 02:54:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:16] ** 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 OK 
test_converters_OpenMStoMSstatsFormat.R    2 tests OK 
test_converters_OpenMStoMSstatsFormat.R    3 tests OK 
test_converters_OpenMStoMSstatsFormat.R    4 tests OK 
test_converters_OpenMStoMSstatsFormat.R    5 tests OK 
test_converters_OpenMStoMSstatsFormat.R    6 tests OK 
test_converters_OpenMStoMSstatsFormat.R    7 tests OK 
test_converters_OpenMStoMSstatsFormat.R    8 tests OK 
test_converters_OpenMStoMSstatsFormat.R    9 tests OK 
test_converters_OpenMStoMSstatsFormat.R   10 tests OK 
test_converters_OpenMStoMSstatsFormat.R   11 tests OK 
test_converters_OpenMStoMSstatsFormat.R   12 tests OK 
test_converters_OpenMStoMSstatsFormat.R   13 tests OK 77ms

test_converters_OpenMStoMSstatsTMTFormat.R    0 tests    INFO  [2026-04-13 02:54:16] ** Raw data from OpenMS imported successfully.
INFO  [2026-04-13 02:54:16] ** Raw data from OpenMS cleaned successfully.
INFO  [2026-04-13 02:54:16] ** 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  [2026-04-13 02:54:16] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** PSMs have been aggregated to peptide ions.
INFO  [2026-04-13 02:54:16] ** For peptides overlapped between fractions of 3_3_3 use the fraction with maximal average abundance.
INFO  [2026-04-13 02:54:16] ** For peptides overlapped between fractions of 2_2_2 use the fraction with maximal average abundance.
INFO  [2026-04-13 02:54:16] ** Fractions belonging to same mixture have been combined.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** Fractionation handled.
INFO  [2026-04-13 02:54:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:16] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_converters_OpenMStoMSstatsTMTFormat.R    0 tests    
test_converters_OpenMStoMSstatsTMTFormat.R    1 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R    2 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R    3 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R    4 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R    5 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R    6 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R    7 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R    8 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R    9 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R   10 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R   11 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R   12 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R   13 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R   13 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R   13 tests OK 
test_converters_OpenMStoMSstatsTMTFormat.R   14 tests OK 0.1s

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  [2026-04-13 02:54:16] ** Raw data from OpenSWATH imported successfully.
INFO  [2026-04-13 02:54:16] ** Raw data from OpenSWATH cleaned successfully.
INFO  [2026-04-13 02:54:16] ** Using provided annotation.
INFO  [2026-04-13 02:54:16] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:16] ** 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  [2026-04-13 02:54:16] ** Rows with values of decoy equal to 1 are removed 
INFO  [2026-04-13 02:54:16] ** Rows with values not smaller than 0.01 in m_score are removed 
INFO  [2026-04-13 02:54:16] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:16] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Fractionation handled.
INFO  [2026-04-13 02:54:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:16] ** 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 OK 
test_converters_OpenSWATHtoMSstatsFormat.R    2 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R    3 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R    4 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R    5 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R    6 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R    7 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R    8 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R    9 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R   10 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R   11 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R   12 tests OK 
test_converters_OpenSWATHtoMSstatsFormat.R   13 tests OK 87ms

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  [2026-04-13 02:54:16] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2026-04-13 02:54:16] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2026-04-13 02:54:16] ** Using provided annotation.
INFO  [2026-04-13 02:54:16] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:16] ** 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  [2026-04-13 02:54:16] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:16] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Fractionation handled.
INFO  [2026-04-13 02:54:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:16] ** 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 OK 
test_converters_PDtoMSstatsFormat.R    2 tests OK 
test_converters_PDtoMSstatsFormat.R    3 tests OK 
test_converters_PDtoMSstatsFormat.R    4 tests OK 
test_converters_PDtoMSstatsFormat.R    5 tests OK 
test_converters_PDtoMSstatsFormat.R    6 tests OK 
test_converters_PDtoMSstatsFormat.R    7 tests OK 
test_converters_PDtoMSstatsFormat.R    8 tests OK 
test_converters_PDtoMSstatsFormat.R    9 tests OK 
test_converters_PDtoMSstatsFormat.R   10 tests OK 
test_converters_PDtoMSstatsFormat.R   11 tests OK 
test_converters_PDtoMSstatsFormat.R   12 tests OK 
test_converters_PDtoMSstatsFormat.R   13 tests OK 73ms

test_converters_PDtoMSstatsTMTFormat.R    0 tests    
test_converters_PDtoMSstatsTMTFormat.R    0 tests    INFO  [2026-04-13 02:54:16] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2026-04-13 02:54:16] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2026-04-13 02:54:16] ** Using provided annotation.
INFO  [2026-04-13 02:54:16] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:16] ** 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  [2026-04-13 02:54:16] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** PSMs have been aggregated to peptide ions.
INFO  [2026-04-13 02:54:16] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** Fractionation handled.
INFO  [2026-04-13 02:54:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:16] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_converters_PDtoMSstatsTMTFormat.R    0 tests    
test_converters_PDtoMSstatsTMTFormat.R    1 tests OK 
test_converters_PDtoMSstatsTMTFormat.R    2 tests OK 
test_converters_PDtoMSstatsTMTFormat.R    3 tests OK 
test_converters_PDtoMSstatsTMTFormat.R    4 tests OK 
test_converters_PDtoMSstatsTMTFormat.R    5 tests OK 
test_converters_PDtoMSstatsTMTFormat.R    6 tests OK 
test_converters_PDtoMSstatsTMTFormat.R    7 tests OK 
test_converters_PDtoMSstatsTMTFormat.R    8 tests OK 
test_converters_PDtoMSstatsTMTFormat.R    9 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   10 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   11 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   12 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   13 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   13 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   13 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   14 tests OK INFO  [2026-04-13 02:54:16] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2026-04-13 02:54:16] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_converters_PDtoMSstatsTMTFormat.R   15 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   15 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   15 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   15 tests OK 
test_converters_PDtoMSstatsTMTFormat.R   16 tests OK 0.2s

test_converters_PhilosophertoMSstatsTMTFormat.R    0 tests    
test_converters_PhilosophertoMSstatsTMTFormat.R    0 tests    INFO  [2026-04-13 02:54:16] ** Raw data from Philosopher imported successfully.
INFO  [2026-04-13 02:54:16] ** Using provided annotation.
INFO  [2026-04-13 02:54:16] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:16] ** 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  [2026-04-13 02:54:16] ** Rows with values not greater than 0.6 in Purity are removed 
WARN  [2026-04-13 02:54:16] ** PeptideProphetProbability not found in input columns.
INFO  [2026-04-13 02:54:16] ** Sequences containing Oxidation are removed.
INFO  [2026-04-13 02:54:16] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** PSMs have been aggregated to peptide ions.
INFO  [2026-04-13 02:54:16] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:16] ** Fractionation handled.
INFO  [2026-04-13 02:54:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:16] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_converters_PhilosophertoMSstatsTMTFormat.R    0 tests    
test_converters_PhilosophertoMSstatsTMTFormat.R    1 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R    2 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R    3 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R    4 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R    5 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R    6 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R    7 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R    8 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R    9 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R   10 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R   11 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R   12 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R   13 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R   13 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R   13 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R   13 tests OK 
test_converters_PhilosophertoMSstatsTMTFormat.R   14 tests OK 0.2s

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  [2026-04-13 02:54:16] ** Raw data from Progenesis imported successfully.
INFO  [2026-04-13 02:54:16] ** Raw data from Progenesis cleaned successfully.
INFO  [2026-04-13 02:54:16] ** Using provided annotation.
INFO  [2026-04-13 02:54:16] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:16] ** 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  [2026-04-13 02:54:16] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:16] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:16] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:16] ** Fractionation handled.
INFO  [2026-04-13 02:54:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:16] ** 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 OK 
test_converters_ProgenesistoMSstatsFormat.R    2 tests OK 
test_converters_ProgenesistoMSstatsFormat.R    3 tests OK 
test_converters_ProgenesistoMSstatsFormat.R    4 tests OK 
test_converters_ProgenesistoMSstatsFormat.R    5 tests OK 
test_converters_ProgenesistoMSstatsFormat.R    6 tests OK 
test_converters_ProgenesistoMSstatsFormat.R    7 tests OK 
test_converters_ProgenesistoMSstatsFormat.R    8 tests OK 
test_converters_ProgenesistoMSstatsFormat.R    9 tests OK 
test_converters_ProgenesistoMSstatsFormat.R   10 tests OK 
test_converters_ProgenesistoMSstatsFormat.R   11 tests OK 
test_converters_ProgenesistoMSstatsFormat.R   12 tests OK 
test_converters_ProgenesistoMSstatsFormat.R   13 tests OK 67ms

test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    
test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    INFO  [2026-04-13 02:54:17] ** Raw data from ProteinProspector imported successfully.
INFO  [2026-04-13 02:54:17] ** Raw data from ProteinProspector cleaned successfully.
INFO  [2026-04-13 02:54:17] ** Using provided annotation.
INFO  [2026-04-13 02:54:17] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:17] ** 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  [2026-04-13 02:54:17] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:17] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:17] ** PSMs have been aggregated to peptide ions.
INFO  [2026-04-13 02:54:17] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:17] ** For peptides overlapped between fractions of Mixture1_1 use the fraction with maximal average abundance.
INFO  [2026-04-13 02:54:17] ** Fractions belonging to same mixture have been combined.
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:17] ** Fractionation handled.
INFO  [2026-04-13 02:54:17] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:17] ** 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 OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    2 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    3 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    4 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    5 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    6 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    7 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    8 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R    9 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   10 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   11 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   12 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   13 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   13 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   14 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   14 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   14 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   14 tests OK 
test_converters_ProteinProspectortoMSstatsTMTFormat.R   15 tests OK 0.2s

test_converters_SkylinetoMSstatsFormat.R    0 tests    
test_converters_SkylinetoMSstatsFormat.R    0 tests    INFO  [2026-04-13 02:54:17] ** Raw data from Skyline imported successfully.
INFO  [2026-04-13 02:54:17] ** Raw data from Skyline cleaned successfully.
INFO  [2026-04-13 02:54:17] ** Using annotation extracted from quantification data.
INFO  [2026-04-13 02:54:17] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:17] ** 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  [2026-04-13 02:54:17] ** Rows with values of StandardType equal to iRT are removed 
INFO  [2026-04-13 02:54:17] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN  [2026-04-13 02:54:17] ** DetectionQValue not found in input columns.
INFO  [2026-04-13 02:54:17] ** Sequences containing DECOY, Decoys are removed.
INFO  [2026-04-13 02:54:17] ** Three isotopic preaks per feature and run are summed
INFO  [2026-04-13 02:54:17] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:17] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:17] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:17] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:17] ** Fractionation handled.
INFO  [2026-04-13 02:54:17] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:17] ** 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 OK 
test_converters_SkylinetoMSstatsFormat.R    2 tests OK 
test_converters_SkylinetoMSstatsFormat.R    3 tests OK 
test_converters_SkylinetoMSstatsFormat.R    4 tests OK 
test_converters_SkylinetoMSstatsFormat.R    5 tests OK 
test_converters_SkylinetoMSstatsFormat.R    6 tests OK 
test_converters_SkylinetoMSstatsFormat.R    7 tests OK 
test_converters_SkylinetoMSstatsFormat.R    8 tests OK 
test_converters_SkylinetoMSstatsFormat.R    9 tests OK 
test_converters_SkylinetoMSstatsFormat.R   10 tests OK 
test_converters_SkylinetoMSstatsFormat.R   11 tests OK 
test_converters_SkylinetoMSstatsFormat.R   12 tests OK 
test_converters_SkylinetoMSstatsFormat.R   13 tests OK 85ms

test_converters_SpectroMinetoMSstatsTMTFormat.R    0 tests    
test_converters_SpectroMinetoMSstatsTMTFormat.R    0 tests    INFO  [2026-04-13 02:54:17] ** Raw data from SpectroMine imported successfully.
INFO  [2026-04-13 02:54:17] ** Raw data from SpectroMine cleaned successfully.
INFO  [2026-04-13 02:54:17] ** Using provided annotation.
INFO  [2026-04-13 02:54:17] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:17] ** 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  [2026-04-13 02:54:17] ** Intensities with values not smaller than 0.01 in PGQValue are replaced with NA
INFO  [2026-04-13 02:54:17] ** Intensities with values not smaller than 0.01 in Qvalue are replaced with NA
INFO  [2026-04-13 02:54:17] ** Features with all missing measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:17] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:17] ** PSMs have been aggregated to peptide ions.
INFO  [2026-04-13 02:54:17] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:17] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2026-04-13 02:54:17] ** Fractions belonging to same mixture have been combined.
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:17] ** Fractionation handled.
INFO  [2026-04-13 02:54:17] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:17] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_converters_SpectroMinetoMSstatsTMTFormat.R    0 tests    
test_converters_SpectroMinetoMSstatsTMTFormat.R    1 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R    2 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R    3 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R    4 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R    5 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R    6 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R    7 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R    8 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R    9 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R   10 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R   11 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R   12 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R   13 tests OK INFO  [2026-04-13 02:54:17] ** Raw data from SpectroMine imported successfully.
INFO  [2026-04-13 02:54:17] ** Raw data from SpectroMine cleaned successfully.
INFO  [2026-04-13 02:54:17] ** Using provided annotation.
INFO  [2026-04-13 02:54:17] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_converters_SpectroMinetoMSstatsTMTFormat.R   14 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R   14 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R   14 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R   14 tests OK 
test_converters_SpectroMinetoMSstatsTMTFormat.R   15 tests OK 0.3s

test_converters_SpectronauttoMSstatsFormat.R    0 tests    
test_converters_SpectronauttoMSstatsFormat.R    0 tests    INFO  [2026-04-13 02:54:17] ** Raw data from Spectronaut imported successfully.
INFO  [2026-04-13 02:54:17] ** Raw data from Spectronaut cleaned successfully.
INFO  [2026-04-13 02:54:17] ** Using annotation extracted from quantification data.
INFO  [2026-04-13 02:54:17] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:17] ** 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  [2026-04-13 02:54:17] ** Intensities with values of FExcludedFromQuantification equal to TRUE are replaced with NA
INFO  [2026-04-13 02:54:17] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:17] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:17] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:17] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:17] ** Fractionation handled.
INFO  [2026-04-13 02:54:17] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:17] ** 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 OK 
test_converters_SpectronauttoMSstatsFormat.R    2 tests OK 
test_converters_SpectronauttoMSstatsFormat.R    3 tests OK 
test_converters_SpectronauttoMSstatsFormat.R    4 tests OK 
test_converters_SpectronauttoMSstatsFormat.R    5 tests OK 
test_converters_SpectronauttoMSstatsFormat.R    6 tests OK 
test_converters_SpectronauttoMSstatsFormat.R    7 tests OK 
test_converters_SpectronauttoMSstatsFormat.R    8 tests OK 
test_converters_SpectronauttoMSstatsFormat.R    9 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   10 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   11 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   12 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   13 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   14 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   14 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   14 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   14 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   15 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   15 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   15 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   15 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   16 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   16 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   16 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   16 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   17 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   17 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   17 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   17 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   17 tests OK INFO  [2026-04-13 02:54:17] ** Raw data from Spectronaut imported successfully.

test_converters_SpectronauttoMSstatsFormat.R   18 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   18 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   18 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   18 tests OK INFO  [2026-04-13 02:54:17] ** Raw data from Spectronaut imported successfully.

test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   19 tests OK INFO  [2026-04-13 02:54:17] ** Raw data from Spectronaut imported successfully.
INFO  [2026-04-13 02:54:17] ** Raw data from Spectronaut cleaned successfully.
INFO  [2026-04-13 02:54:17] ** Using annotation extracted from quantification data.
INFO  [2026-04-13 02:54:17] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:17] ** 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  [2026-04-13 02:54:17] ** Intensities with values of FExcludedFromQuantification equal to TRUE are replaced with NA
INFO  [2026-04-13 02:54:17] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:17] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:17] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:17] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:17] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:17] ** Fractionation handled.
INFO  [2026-04-13 02:54:17] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:18] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_SpectronauttoMSstatsFormat.R   19 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   20 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   21 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   22 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   23 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   24 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   25 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   26 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   27 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   28 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   29 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   30 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   31 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   32 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   33 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   34 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   35 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   36 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   37 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   38 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   39 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   40 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   41 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   42 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   43 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   44 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   45 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   46 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   47 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   48 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   49 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   50 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   51 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   52 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   52 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   52 tests OK INFO  [2026-04-13 02:54:18] ** Raw data from Spectronaut imported successfully.
INFO  [2026-04-13 02:54:18] ** Raw data from Spectronaut cleaned successfully.
INFO  [2026-04-13 02:54:18] ** Using annotation extracted from quantification data.
INFO  [2026-04-13 02:54:18] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:18] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType
  - 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  [2026-04-13 02:54:18] ** Intensities with values of FExcludedFromQuantification equal to TRUE are replaced with NA
WARN  [2026-04-13 02:54:18] ** PGQvalue not found in input columns.
WARN  [2026-04-13 02:54:18] ** EGQvalue not found in input columns.
INFO  [2026-04-13 02:54:18] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:18] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:18] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:18] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:18] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:18] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:18] ** Fractionation handled.
INFO  [2026-04-13 02:54:18] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:18] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_SpectronauttoMSstatsFormat.R   52 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   53 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   54 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   55 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   56 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   57 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   58 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   59 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   60 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   61 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   62 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   63 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   64 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   65 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   66 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   67 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   67 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   68 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   68 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   69 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   69 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   70 tests OK INFO  [2026-04-13 02:54:18] ** Raw data from Spectronaut imported successfully.
INFO  [2026-04-13 02:54:18] ** Raw data from Spectronaut cleaned successfully.
INFO  [2026-04-13 02:54:18] ** Using annotation extracted from quantification data.
INFO  [2026-04-13 02:54:18] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2026-04-13 02:54:18] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType
  - 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  [2026-04-13 02:54:18] ** Intensities with values of FExcludedFromQuantification equal to TRUE are replaced with NA
WARN  [2026-04-13 02:54:18] ** PGQvalue not found in input columns.
WARN  [2026-04-13 02:54:18] ** EGQvalue not found in input columns.
INFO  [2026-04-13 02:54:18] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:18] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:18] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:18] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:18] ** Run annotation merged with quantification data.
INFO  [2026-04-13 02:54:18] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:18] ** Fractionation handled.
INFO  [2026-04-13 02:54:18] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2026-04-13 02:54:18] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_SpectronauttoMSstatsFormat.R   70 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   71 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   71 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   71 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   71 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   72 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   72 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   72 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   73 tests OK 1.2s

test_dt.R.....................    0 tests    
test_dt.R.....................    0 tests    
test_dt.R.....................    1 tests OK 
test_dt.R.....................    2 tests OK 
test_dt.R.....................    3 tests OK 
test_dt.R.....................    4 tests OK 
test_dt.R.....................    5 tests OK 
test_dt.R.....................    6 tests OK 
test_dt.R.....................    7 tests OK 
test_dt.R.....................    7 tests OK 
test_dt.R.....................    8 tests OK 
test_dt.R.....................    8 tests OK 
test_dt.R.....................    8 tests OK 
test_dt.R.....................    9 tests OK 
test_dt.R.....................   10 tests OK 
test_dt.R.....................   11 tests OK 11ms

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  [2026-04-13 02:54:18] ** Features with one or two measurements across channels within each run are removed.

test_feature_cleaning.R.......    1 tests OK INFO  [2026-04-13 02:54:18] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    2 tests OK INFO  [2026-04-13 02:54:18] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    3 tests OK 
test_feature_cleaning.R.......    3 tests OK 
test_feature_cleaning.R.......    3 tests OK INFO  [2026-04-13 02:54:18] ** Features with all missing measurements across runs are removed.

test_feature_cleaning.R.......    4 tests OK INFO  [2026-04-13 02:54:18] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    5 tests OK 
test_feature_cleaning.R.......    5 tests OK 
test_feature_cleaning.R.......    5 tests OK 
test_feature_cleaning.R.......    6 tests OK 
test_feature_cleaning.R.......    6 tests OK 
test_feature_cleaning.R.......    6 tests OK 
test_feature_cleaning.R.......    6 tests OK 
test_feature_cleaning.R.......    7 tests OK INFO  [2026-04-13 02:54:18] ** Three isotopic preaks per feature and run are summed

test_feature_cleaning.R.......    8 tests OK 
test_feature_cleaning.R.......    9 tests OK 
test_feature_cleaning.R.......    9 tests OK 
test_feature_cleaning.R.......    9 tests OK 
test_feature_cleaning.R.......    9 tests OK 
test_feature_cleaning.R.......    9 tests OK 
test_feature_cleaning.R.......    9 tests OK 
test_feature_cleaning.R.......    9 tests OK 
test_feature_cleaning.R.......    9 tests OK 
test_feature_cleaning.R.......    9 tests OK 
test_feature_cleaning.R.......   10 tests OK 
test_feature_cleaning.R.......   10 tests OK 
test_feature_cleaning.R.......   10 tests OK 
test_feature_cleaning.R.......   11 tests OK 
test_feature_cleaning.R.......   11 tests OK 
test_feature_cleaning.R.......   11 tests OK 
test_feature_cleaning.R.......   12 tests OK 
test_feature_cleaning.R.......   12 tests OK 
test_feature_cleaning.R.......   13 tests OK 
test_feature_cleaning.R.......   13 tests OK 
test_feature_cleaning.R.......   14 tests OK 
test_feature_cleaning.R.......   14 tests OK 
test_feature_cleaning.R.......   14 tests OK 
test_feature_cleaning.R.......   14 tests OK 
test_feature_cleaning.R.......   14 tests OK 
test_feature_cleaning.R.......   14 tests OK 
test_feature_cleaning.R.......   15 tests OK 
test_feature_cleaning.R.......   15 tests OK INFO  [2026-04-13 02:54:18] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests OK INFO  [2026-04-13 02:54:19] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests OK 
test_feature_cleaning.R.......   17 tests OK 
test_feature_cleaning.R.......   17 tests OK 
test_feature_cleaning.R.......   17 tests OK 
test_feature_cleaning.R.......   18 tests OK INFO  [2026-04-13 02:54:19] Proteins with a single feature are removed.

test_feature_cleaning.R.......   19 tests OK 
test_feature_cleaning.R.......   20 tests OK INFO  [2026-04-13 02:54:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:19] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......   20 tests OK INFO  [2026-04-13 02:54:19] ** Features with one or two measurements across channels within each run are removed.
INFO  [2026-04-13 02:54:19] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   20 tests OK 
test_feature_cleaning.R.......   21 tests OK 
test_feature_cleaning.R.......   22 tests OK 0.3s

test_filtering.R..............    0 tests    
test_filtering.R..............    0 tests    
test_filtering.R..............    1 tests OK INFO  [2026-04-13 02:54:19] ** Sequences containing \+ are removed.

test_filtering.R..............    2 tests OK INFO  [2026-04-13 02:54:19] ** Sequences containing \+ are removed.

test_filtering.R..............    3 tests OK 
test_filtering.R..............    4 tests OK 
test_filtering.R..............    5 tests OK 
test_filtering.R..............    6 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_1 equal to - are removed 

test_filtering.R..............    7 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_1 equal to +, - are removed 

test_filtering.R..............    8 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_1 equal to + are removed 

test_filtering.R..............    9 tests OK 
test_filtering.R..............   10 tests OK 
test_filtering.R..............   11 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_1 equal to R are removed 

test_filtering.R..............   12 tests OK 
test_filtering.R..............   13 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_2 equal to + are removed 

test_filtering.R..............   14 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_2 equal to X are removed 

test_filtering.R..............   15 tests OK 
test_filtering.R..............   16 tests OK 
test_filtering.R..............   17 tests OK 
test_filtering.R..............   18 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   19 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   20 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   21 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   22 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   23 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   24 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   25 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   26 tests OK INFO  [2026-04-13 02:54:19] ** Intensities with values not greater than 0.3 in Score are replaced with NA

test_filtering.R..............   26 tests OK 
test_filtering.R..............   27 tests OK 
test_filtering.R..............   28 tests OK INFO  [2026-04-13 02:54:19] ** Intensities with values not greater than 0.3 in Score are replaced with NA

test_filtering.R..............   28 tests OK 
test_filtering.R..............   29 tests OK 
test_filtering.R..............   30 tests OK INFO  [2026-04-13 02:54:19] ** Intensities with values not smaller than 0.3 in Score are replaced with NA

test_filtering.R..............   30 tests OK 
test_filtering.R..............   31 tests OK 
test_filtering.R..............   32 tests OK INFO  [2026-04-13 02:54:19] ** Intensities with values not smaller than 0.3 in Score are replaced with NA

test_filtering.R..............   32 tests OK 
test_filtering.R..............   33 tests OK 
test_filtering.R..............   34 tests OK 
test_filtering.R..............   35 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2026-04-13 02:54:19] ** Sequences containing \+ are removed.

test_filtering.R..............   36 tests OK INFO  [2026-04-13 02:54:19] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2026-04-13 02:54:19] ** Sequences containing \+ are removed.

test_filtering.R..............   37 tests OK 48ms

test_fractions.R..............    0 tests    
test_fractions.R..............    1 tests OK 
test_fractions.R..............    1 tests OK 
test_fractions.R..............    1 tests OK 
test_fractions.R..............    1 tests OK 
test_fractions.R..............    1 tests OK 
test_fractions.R..............    1 tests OK 
test_fractions.R..............    2 tests OK 
test_fractions.R..............    3 tests OK 
test_fractions.R..............    4 tests OK 
test_fractions.R..............    4 tests OK 
test_fractions.R..............    5 tests OK 
test_fractions.R..............    5 tests OK 
test_fractions.R..............    6 tests OK 
test_fractions.R..............    7 tests OK 
test_fractions.R..............    8 tests OK 
test_fractions.R..............    8 tests OK 
test_fractions.R..............    9 tests OK 
test_fractions.R..............    9 tests OK 
test_fractions.R..............   10 tests OK 
test_fractions.R..............   11 tests OK 
test_fractions.R..............   12 tests OK 
test_fractions.R..............   13 tests OK 
test_fractions.R..............   13 tests OK 
test_fractions.R..............   14 tests OK 
test_fractions.R..............   14 tests OK 
test_fractions.R..............   15 tests OK 
test_fractions.R..............   15 tests OK INFO  [2026-04-13 02:54:19] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2026-04-13 02:54:19] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2026-04-13 02:54:19] ** For peptides overlapped between fractions of 2_1 use the fraction with maximal average abundance.

test_fractions.R..............   15 tests OK 
test_fractions.R..............   16 tests OK 0.2s

test_logging.R................    1 tests OK 
test_logging.R................    2 tests OK 
test_logging.R................    3 tests OK 2ms

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2026-04-13 02:54:19] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2026-04-13 02:54:19] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    1 tests OK 
test_shared_peptides.R........    2 tests OK 
test_shared_peptides.R........    3 tests OK 
test_shared_peptides.R........    4 tests OK 
test_shared_peptides.R........    5 tests OK 13ms

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 OK 
test_utils_anomaly_score.R....    1 tests OK 
test_utils_anomaly_score.R....    1 tests OK 
test_utils_anomaly_score.R....    2 tests OK 
test_utils_anomaly_score.R....    3 tests OK 
test_utils_anomaly_score.R....    3 tests OK 
test_utils_anomaly_score.R....    3 tests OK 
test_utils_anomaly_score.R....    3 tests OK 
test_utils_anomaly_score.R....    3 tests OK 
test_utils_anomaly_score.R....    4 tests OK 
test_utils_anomaly_score.R....    4 tests OK 
test_utils_anomaly_score.R....    4 tests OK 
test_utils_anomaly_score.R....    4 tests OK 
test_utils_anomaly_score.R....    5 tests OK 
test_utils_anomaly_score.R....    5 tests OK 
test_utils_anomaly_score.R....    5 tests OK 
test_utils_anomaly_score.R....    6 tests OK 
test_utils_anomaly_score.R....    6 tests OK 
test_utils_anomaly_score.R....    6 tests OK 
test_utils_anomaly_score.R....    6 tests OK 
test_utils_anomaly_score.R....    6 tests OK 
test_utils_anomaly_score.R....    6 tests OK 
test_utils_anomaly_score.R....    7 tests OK 
test_utils_anomaly_score.R....    7 tests OK 
test_utils_anomaly_score.R....    7 tests OK 
test_utils_anomaly_score.R....    8 tests OK 
test_utils_anomaly_score.R....    8 tests OK 
test_utils_anomaly_score.R....    8 tests OK 
test_utils_anomaly_score.R....    9 tests OK 
test_utils_anomaly_score.R....    9 tests OK 
test_utils_anomaly_score.R....    9 tests OK 
test_utils_anomaly_score.R....    9 tests OK 
test_utils_anomaly_score.R....    9 tests OK 
test_utils_anomaly_score.R....    9 tests OK 
test_utils_anomaly_score.R....   10 tests OK 
test_utils_anomaly_score.R....   10 tests OK 
test_utils_anomaly_score.R....   11 tests OK 
test_utils_anomaly_score.R....   12 tests OK 
test_utils_anomaly_score.R....   13 tests OK 
test_utils_anomaly_score.R....   14 tests OK Top 5 anomalous rows: 20 12 15 11 10 

test_utils_anomaly_score.R....   14 tests OK Score range: 0.3062677 0.5660067 

test_utils_anomaly_score.R....   14 tests OK 
test_utils_anomaly_score.R....   14 tests OK 
test_utils_anomaly_score.R....   14 tests OK 
test_utils_anomaly_score.R....   15 tests OK 
test_utils_anomaly_score.R....   16 tests OK 
test_utils_anomaly_score.R....   16 tests OK 
test_utils_anomaly_score.R....   16 tests OK 
test_utils_anomaly_score.R....   17 tests OK 
test_utils_anomaly_score.R....   18 tests OK 
test_utils_anomaly_score.R....   19 tests OK 
test_utils_anomaly_score.R....   19 tests OK 
test_utils_anomaly_score.R....   19 tests OK 
test_utils_anomaly_score.R....   19 tests OK 
test_utils_anomaly_score.R....   19 tests OK 
test_utils_anomaly_score.R....   20 tests OK 
test_utils_anomaly_score.R....   21 tests OK 
test_utils_anomaly_score.R....   22 tests OK All anomaly detection tests completed successfully!

test_utils_anomaly_score.R....   22 tests OK 
test_utils_anomaly_score.R....   22 tests OK 
test_utils_anomaly_score.R....   22 tests OK 
test_utils_anomaly_score.R....   22 tests OK 
test_utils_anomaly_score.R....   22 tests OK 
test_utils_anomaly_score.R....   22 tests OK 
test_utils_anomaly_score.R....   23 tests OK 
test_utils_anomaly_score.R....   24 tests OK 
test_utils_anomaly_score.R....   24 tests OK 
test_utils_anomaly_score.R....   25 tests OK 
test_utils_anomaly_score.R....   26 tests OK 
test_utils_anomaly_score.R....   26 tests OK 
test_utils_anomaly_score.R....   27 tests OK 7.9s

test_utils_data_health.R......    0 tests    
test_utils_data_health.R......    0 tests    INFO  [2026-04-13 02:54:27] 0% of the values are missing across all intensities

test_utils_data_health.R......    0 tests    
test_utils_data_health.R......    1 tests OK 
test_utils_data_health.R......    2 tests OK 
test_utils_data_health.R......    2 tests OK 
test_utils_data_health.R......    2 tests OK INFO  [2026-04-13 02:54:27] 20% of the values are missing across all intensities

test_utils_data_health.R......    2 tests OK 
test_utils_data_health.R......    3 tests OK 
test_utils_data_health.R......    3 tests OK 
test_utils_data_health.R......    3 tests OK INFO  [2026-04-13 02:54:27] 100% of the values are missing across all intensities

test_utils_data_health.R......    3 tests OK 
test_utils_data_health.R......    4 tests OK 
test_utils_data_health.R......    4 tests OK INFO  [2026-04-13 02:54:27] Intensity distribution standard truncated data.

test_utils_data_health.R......    4 tests OK 
test_utils_data_health.R......    5 tests OK 
test_utils_data_health.R......    5 tests OK 
test_utils_data_health.R......    5 tests OK INFO  [2026-04-13 02:54:27] Intensity distribution indicates zero truncated data. More missing values than normal should be expected.

test_utils_data_health.R......    5 tests OK 
test_utils_data_health.R......    6 tests OK 
test_utils_data_health.R......    6 tests OK 
test_utils_data_health.R......    6 tests OK INFO  [2026-04-13 02:54:27] 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 OK 
test_utils_data_health.R......    7 tests OK 
test_utils_data_health.R......    8 tests OK 
test_utils_data_health.R......    9 tests OK 
test_utils_data_health.R......   10 tests OK 
test_utils_data_health.R......   11 tests OK 
test_utils_data_health.R......   11 tests OK 
test_utils_data_health.R......   12 tests OK 
test_utils_data_health.R......   13 tests OK 
test_utils_data_health.R......   14 tests OK 
test_utils_data_health.R......   15 tests OK 
test_utils_data_health.R......   15 tests OK 
test_utils_data_health.R......   15 tests OK INFO  [2026-04-13 02:54:27] 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 OK INFO  [2026-04-13 02:54:27] 0% of all measured intensities fall within the outlier range

test_utils_data_health.R......   15 tests OK 
test_utils_data_health.R......   16 tests OK 
test_utils_data_health.R......   17 tests OK 
test_utils_data_health.R......   17 tests OK 
test_utils_data_health.R......   17 tests OK 
test_utils_data_health.R......   18 tests OK 
test_utils_data_health.R......   19 tests OK 
test_utils_data_health.R......   20 tests OK 
test_utils_data_health.R......   21 tests OK 
test_utils_data_health.R......   21 tests OK 
test_utils_data_health.R......   21 tests OK INFO  [2026-04-13 02:54:27] 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 OK INFO  [2026-04-13 02:54:27] 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 OK 
test_utils_data_health.R......   22 tests OK 
test_utils_data_health.R......   23 tests OK 
test_utils_data_health.R......   24 tests OK 
test_utils_data_health.R......   24 tests OK 
test_utils_data_health.R......   24 tests OK INFO  [2026-04-13 02:54:27] 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 OK 
test_utils_data_health.R......   24 tests OK 
test_utils_data_health.R......   24 tests OK 
test_utils_data_health.R......   25 tests OK 
test_utils_data_health.R......   25 tests OK 
test_utils_data_health.R......   25 tests OK 
test_utils_data_health.R......   26 tests OK 
test_utils_data_health.R......   26 tests OK 
test_utils_data_health.R......   26 tests OK 
test_utils_data_health.R......   27 tests OK 
test_utils_data_health.R......   27 tests OK 
test_utils_data_health.R......   27 tests OK 
test_utils_data_health.R......   28 tests OK 
test_utils_data_health.R......   28 tests OK 
test_utils_data_health.R......   28 tests OK 
test_utils_data_health.R......   29 tests OK 
test_utils_data_health.R......   30 tests OK 
test_utils_data_health.R......   31 tests OK 
test_utils_data_health.R......   31 tests OK 
test_utils_data_health.R......   32 tests OK 
test_utils_data_health.R......   33 tests OK 
test_utils_data_health.R......   34 tests OK 
test_utils_data_health.R......   34 tests OK 
test_utils_data_health.R......   35 tests OK 
test_utils_data_health.R......   35 tests OK INFO  [2026-04-13 02:54:27] 0% of the values are missing across all intensities
INFO  [2026-04-13 02:54:27] Intensity distribution standard truncated data.
INFO  [2026-04-13 02:54:27] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2026-04-13 02:54:27] 0% of all measured intensities fall within the outlier range
INFO  [2026-04-13 02:54:27] 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 OK 
test_utils_data_health.R......   36 tests OK 
test_utils_data_health.R......   37 tests OK 
test_utils_data_health.R......   37 tests OK 
test_utils_data_health.R......   37 tests OK 
test_utils_data_health.R......   38 tests OK 
test_utils_data_health.R......   38 tests OK 
test_utils_data_health.R......   39 tests OK 
test_utils_data_health.R......   40 tests OK 
test_utils_data_health.R......   41 tests OK 
test_utils_data_health.R......   41 tests OK 
test_utils_data_health.R......   42 tests OK 
test_utils_data_health.R......   42 tests OK 
test_utils_data_health.R......   42 tests OK INFO  [2026-04-13 02:54:27] 0% of the values are missing across all intensities
INFO  [2026-04-13 02:54:27] Intensity distribution standard truncated data.
INFO  [2026-04-13 02:54:27] 0% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2026-04-13 02:54:27] 0% of all measured intensities fall within the outlier range
INFO  [2026-04-13 02:54:27] 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 OK 
test_utils_data_health.R......   43 tests OK 
test_utils_data_health.R......   43 tests OK 
test_utils_data_health.R......   44 tests OK 
test_utils_data_health.R......   44 tests OK 
test_utils_data_health.R......   44 tests OK 
test_utils_data_health.R......   44 tests OK INFO  [2026-04-13 02:54:27] 0% of the values are missing across all intensities
INFO  [2026-04-13 02:54:27] Intensity distribution standard truncated data.
INFO  [2026-04-13 02:54:27] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2026-04-13 02:54:27] 0% of all measured intensities fall within the outlier range
INFO  [2026-04-13 02:54:27] 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 OK 
test_utils_data_health.R......   44 tests OK 
test_utils_data_health.R......   45 tests OK 
test_utils_data_health.R......   46 tests OK 
test_utils_data_health.R......   46 tests OK 
test_utils_data_health.R......   46 tests OK INFO  [2026-04-13 02:54:27] 0% of the values are missing across all intensities
INFO  [2026-04-13 02:54:27] Intensity distribution standard truncated data.
INFO  [2026-04-13 02:54:27] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2026-04-13 02:54:27] 0% of all measured intensities fall within the outlier range
INFO  [2026-04-13 02:54:27] 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 OK 
test_utils_data_health.R......   46 tests OK 
test_utils_data_health.R......   47 tests OK 
test_utils_data_health.R......   47 tests OK 
test_utils_data_health.R......   47 tests OK 
test_utils_data_health.R......   47 tests OK INFO  [2026-04-13 02:54:27] 0% of the values are missing across all intensities
INFO  [2026-04-13 02:54:27] Intensity distribution standard truncated data.
INFO  [2026-04-13 02:54:27] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2026-04-13 02:54:27] 0% of all measured intensities fall within the outlier range
INFO  [2026-04-13 02:54:27] 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 OK 
test_utils_data_health.R......   47 tests OK 
test_utils_data_health.R......   48 tests OK 
test_utils_data_health.R......   49 tests OK 0.2s

test_workflow.R...............    0 tests    
test_workflow.R...............    0 tests    INFO  [2026-04-13 02:54:27] ** Raw data from OpenMS imported successfully.

test_workflow.R...............    0 tests    
test_workflow.R...............    1 tests OK INFO  [2026-04-13 02:54:27] ** Raw data from OpenMS cleaned successfully.

test_workflow.R...............    1 tests OK 
test_workflow.R...............    2 tests OK INFO  [2026-04-13 02:54:27] ** Using annotation extracted from quantification data.
INFO  [2026-04-13 02:54:27] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_workflow.R...............    2 tests OK 
test_workflow.R...............    3 tests OK INFO  [2026-04-13 02:54:27] ** 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  [2026-04-13 02:54:27] ** Features with all missing measurements across runs are removed.
INFO  [2026-04-13 02:54:27] ** Shared peptides are removed.
INFO  [2026-04-13 02:54:27] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2026-04-13 02:54:27] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:27] Proteins with a single feature are removed.
INFO  [2026-04-13 02:54:27] ** Run annotation merged with quantification data.

test_workflow.R...............    3 tests OK 
test_workflow.R...............    4 tests OK 
test_workflow.R...............    5 tests OK 
test_workflow.R...............    6 tests OK INFO  [2026-04-13 02:54:27] ** Features with one or two measurements across runs are removed.
INFO  [2026-04-13 02:54:27] ** Fractionation handled.
INFO  [2026-04-13 02:54:27] ** Updated quantification data to make balanced design. Missing values are marked by NA

test_workflow.R...............    6 tests OK 
test_workflow.R...............    7 tests OK 
test_workflow.R...............    8 tests OK 96ms
All ok, 630 results (14.0s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> 
> proc.time()
   user  system elapsed 
  7.360   0.547  14.615

Example timings

MSstatsConvert.Rcheck/MSstatsConvert-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsFormat0.8090.0580.848
DIAUmpiretoMSstatsFormat0.1130.0010.100
FragPipetoMSstatsFormat0.0640.0030.056
MSstatsBalancedDesign0.0260.0010.028
MSstatsClean0.1020.0000.086
MSstatsImport0.0720.0040.073
MSstatsLogsSettings0.0110.0010.012
MSstatsMakeAnnotation0.1490.0040.134
MSstatsPreprocess0.1470.0200.133
MSstatsSaveSessionInfo0.0180.0110.029
MaxQtoMSstatsFormat0.1940.0180.127
MaxQtoMSstatsTMTFormat0.2120.0160.156
MetamorpheusToMSstatsFormat0.0700.0050.065
OpenMStoMSstatsFormat0.0800.0030.069
OpenMStoMSstatsTMTFormat0.1800.0060.160
OpenSWATHtoMSstatsFormat0.1450.0040.130
PDtoMSstatsFormat0.0930.0020.075
PDtoMSstatsTMTFormat0.3260.0030.218
PhilosophertoMSstatsTMTFormat0.1810.0050.176
ProgenesistoMSstatsFormat0.0840.0040.070
ProteinProspectortoMSstatsTMTFormat0.2750.0030.252
SkylinetoMSstatsFormat0.1370.0040.103
SpectroMinetoMSstatsTMTFormat0.3270.0070.278
SpectronauttoMSstatsFormat0.0930.0010.072
getDataType0.0640.0020.066
getInputFile0.0680.0030.071