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This page was generated on 2025-10-23 12:04 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4684
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4629
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 1395/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsConvert 1.19.3  (landing page)
Mateusz Staniak
Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025)
git_url: https://git.bioconductor.org/packages/MSstatsConvert
git_branch: devel
git_last_commit: c7756a9
git_last_commit_date: 2025-09-27 11:07:54 -0400 (Sat, 27 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  

CHECK results for MSstatsConvert on nebbiolo2

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

raw results


Summary

Package: MSstatsConvert
Version: 1.19.3
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MSstatsConvert_1.19.3.tar.gz
StartedAt: 2025-10-23 02:23:44 -0400 (Thu, 23 Oct 2025)
EndedAt: 2025-10-23 02:24:29 -0400 (Thu, 23 Oct 2025)
EllapsedTime: 45.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsConvert.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MSstatsConvert_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MSstatsConvert.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK
* this is package ‘MSstatsConvert’ version ‘1.19.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsConvert’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs       1.9Mb
    tinytest   6.1Mb
* 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
.checkAnomalySkew: no visible global function definition for ‘.’
.checkAnomalySkew: no visible binding for global variable
  ‘AnomalyScores’
.checkAnomalySkew: no visible binding for global variable ‘PSM’
.checkFeatureCoverage: no visible global function definition for ‘.’
.checkFeatureCoverage: no visible binding for global variable
  ‘Intensity’
.checkFeatureCoverage: no visible binding for global variable ‘Feature’
.checkFeatureOutliers: no visible binding for global variable
  ‘is_outlier’
.checkFeatureOutliers: no visible binding for global variable
  ‘Intensity’
.checkFeatureOutliers: no visible binding for global variable
  ‘mean_Intensity’
.checkFeatureOutliers: no visible binding for global variable
  ‘sd_Intensity’
.checkFeatureOutliers: no visible global function definition for ‘.’
.checkFeatureOutliers: no visible binding for global variable ‘Feature’
.checkFeatureSD: no visible global function definition for ‘.’
.checkFeatureSD: no visible global function definition for ‘sd’
.checkFeatureSD: no visible binding for global variable ‘Intensity’
.checkFeatureSD: no visible binding for global variable ‘Feature’
.checkIntensityDistribution: no visible global function definition for
  ‘sd’
.cleanDIANNAddMissingColumns: no visible binding for global variable
  ‘PrecursorMz’
.cleanDIANNAddMissingColumns: no visible binding for global variable
  ‘FragmentInfo’
.cleanDIANNCleanAndFilterData: no visible binding for global variable
  ‘FragmentIon’
.cleanDIANNProcessFragmentInfo: no visible binding for global variable
  ‘FragmentInfo’
.cleanDIANNProcessFragmentInfo: no visible binding for global variable
  ‘FragmentIon’
.cleanDIANNProcessFragmentInfo: no visible binding for global variable
  ‘ProductCharge’
.cleanDIANNProcessQuantificationColumns: no visible binding for global
  variable ‘FragmentQuantCorrected’
.cleanDIANNRenameColumns: no visible binding for global variable
  ‘PeptideSequence’
.cleanRawPhilosopher: no visible binding for global variable ‘Run’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘Intensity’
.prepareSpectronautAnomalyInput: no visible global function definition
  for ‘.’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘Fragment’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘count’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘ProteinName’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘feature_rank’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘MeanAbundance’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘..cols’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘PSM’
.prepareSpectronautAnomalyInput: no visible binding for global variable
  ‘Order’
.runAnomalyModel : <anonymous>: no visible binding for global variable
  ‘..quality_metrics’
.summarizeMultipleMeasurements: no visible binding for global variable
  ‘row_id’
.summarizeMultipleMeasurements: no visible global function definition
  for ‘.’
.summarizeMultiplePSMs: no visible binding for global variable ‘Purity’
.summarizeMultiplePSMs: no visible binding for global variable
  ‘PeptideProphet.Probability’
.validateMSstatsConverterParameters: no visible global function
  definition for ‘modifyList’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘DetectionQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalQValue’
MSstatsAnomalyScores: no visible binding for global variable
  ‘..subset_cols’
SkylinetoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
SpectronauttoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
pearson_skewness: no visible global function definition for ‘sd’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘Run’
Undefined global functions or variables:
  . ..cols ..quality_metrics ..subset_cols AnomalyScores
  DetectionQValue Feature Fragment FragmentInfo FragmentIon
  FragmentQuantCorrected GlobalPGQValue GlobalQValue Intensity
  LibPGQValue LibQValue MeanAbundance Order PSM
  PeptideProphet.Probability PeptideSequence PrecursorMz ProductCharge
  ProteinName Purity Run count feature_rank is_outlier mean_Intensity
  modifyList row_id sd sd_Intensity
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'dot-getFullDesign.Rd':
  ‘`feature_col`’ ‘`measurement_col`’

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MSstatsConvert.Rcheck/00check.log’
for details.

Installation output

MSstatsConvert.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MSstatsConvert
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MSstatsConvert’ ...
** this is package ‘MSstatsConvert’ version ‘1.19.3’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o MSstatsConvert.so RcppExports.o isolation_forest.o -fopenmp -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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 65ms

test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    
test_annotation.R.............    0 tests    INFO  [2025-10-23 02:24:11] ** Using annotation extracted from quantification data.
INFO  [2025-10-23 02:24:11] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    1 tests OK INFO  [2025-10-23 02:24:11] ** Using provided annotation.
INFO  [2025-10-23 02:24:11] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    2 tests OK 
test_annotation.R.............    2 tests OK INFO  [2025-10-23 02:24:11] ** Using provided annotation.
INFO  [2025-10-23 02:24:11] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    3 tests OK INFO  [2025-10-23 02:24:11] ** Using provided annotation.
INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Run annotation merged with quantification data.

test_annotation.R.............    6 tests OK INFO  [2025-10-23 02:24:11] ** Using provided annotation.
INFO  [2025-10-23 02:24:11] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    6 tests OK INFO  [2025-10-23 02:24:11] ** Run annotation merged with quantification data.

test_annotation.R.............    7 tests OK INFO  [2025-10-23 02:24:11] ** Using provided annotation.
INFO  [2025-10-23 02:24:11] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    7 tests OK 
test_annotation.R.............    8 tests OK INFO  [2025-10-23 02:24:11] ** Using provided annotation.
INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Using provided annotation.

test_annotation.R.............   11 tests OK 0.1s

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 53ms

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2025-10-23 02:24:11] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-10-23 02:24:11] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-10-23 02:24:11] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2025-10-23 02:24:11] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-10-23 02:24:11] ** Using selected fragments and peptides.
INFO  [2025-10-23 02:24:11] ** Extracted the data from selected fragments and/or peptides.
INFO  [2025-10-23 02:24:11] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-10-23 02:24:11] ** Using selected fragments and peptides.
INFO  [2025-10-23 02:24:11] ** Extracted the data from selected fragments and/or peptides.
INFO  [2025-10-23 02:24:11] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2025-10-23 02:24:11] ** Using selected fragments.
INFO  [2025-10-23 02:24:11] ** Extracted the data from selected fragments and/or peptides.
INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2025-10-23 02:24:11] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:11] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2025-10-23 02:24:11] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2025-10-23 02:24:11] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2025-10-23 02:24:11] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:11] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............   13 tests OK INFO  [2025-10-23 02:24:11] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:11] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:11] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2025-10-23 02:24:11] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   15 tests OK 
test_cleanRaw.R...............   16 tests OK INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   18 tests OK INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Raw data from OpenSWATH imported successfully.

test_cleanRaw.R...............   20 tests OK INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK 
test_cleanRaw.R...............   30 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2025-10-23 02:24:11] ** 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  [2025-10-23 02:24:11] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2025-10-23 02:24:11] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2025-10-23 02:24:12] ** 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  [2025-10-23 02:24:12] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   37 tests OK 
test_cleanRaw.R...............   37 tests OK INFO  [2025-10-23 02:24:12] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2025-10-23 02:24:12] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2025-10-23 02:24:12] ** 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 [2025-10-23 02:24:12] 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  [2025-10-23 02:24:12] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2025-10-23 02:24:12] ** 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  [2025-10-23 02:24:12] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   42 tests OK INFO  [2025-10-23 02:24:12] ** 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  [2025-10-23 02:24:12] ** Raw data from Metamorpheus imported successfully.

test_cleanRaw.R...............   44 tests OK 
test_cleanRaw.R...............   45 tests OK 0.6s

test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............    0 tests    INFO  [2025-10-23 02:24:12] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............   15 tests OK INFO  [2025-10-23 02:24:12] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............   15 tests OK 
test_clean_DIANN.R............   30 tests OK 46ms

test_clean_Metamorpheus.R.....    0 tests    
test_clean_Metamorpheus.R.....    0 tests    INFO  [2025-10-23 02:24:12] ** 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 6ms

test_clean_ProteinProspector.R    0 tests    
test_clean_ProteinProspector.R    0 tests    
test_clean_ProteinProspector.R    0 tests    INFO  [2025-10-23 02:24:12] ** Raw data from ProteinProspector cleaned successfully.

test_clean_ProteinProspector.R    3 tests OK 12ms

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_converters_DIANNtoMSstatsFormat.R    0 tests    
test_converters_DIANNtoMSstatsFormat.R    0 tests    
test_converters_DIANNtoMSstatsFormat.R    0 tests    
test_converters_DIANNtoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:12] ** Raw data from DIANN imported successfully.
INFO  [2025-10-23 02:24:12] ** Raw data from DIANN cleaned successfully.
INFO  [2025-10-23 02:24:12] ** Using provided annotation.
INFO  [2025-10-23 02:24:12] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:12] ** Filtering on Global Q Value < 0.01
INFO  [2025-10-23 02:24:12] ** MBR was not used to analyze the data. Now setting names and filtering
INFO  [2025-10-23 02:24:12] -- Filtering on GlobalPGQValue < 0.01
INFO  [2025-10-23 02:24:12] -- Filtering on GlobalQValue < 0.01
INFO  [2025-10-23 02:24:12] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:12] ** Sequences containing DECOY, Decoys are removed.
INFO  [2025-10-23 02:24:12] ** Sequences containing \(UniMod\:35\) are removed.
INFO  [2025-10-23 02:24:12] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:12] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:12] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:12] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:12] Proteins with a single feature are removed.
INFO  [2025-10-23 02:24:12] ** Run annotation merged with quantification data.
WARN  [2025-10-23 02:24:12] The following features have missing values in at least one run. AESTDDVDYIMR_2_Frag1_1,
 AESTDDVDYIMR_2_Frag2_1,
 AGWEAYLR_2_Frag1_1,
 AGWEAYLR_2_Frag2_1,
 AGWEAYLR_2_Frag3_1,
 AGWEAYLR_2_Frag4_1,
 AIDEQFGSLDELIK_2_Frag1_1,
 AIDEQFGSLDELIK_2_Frag2_1,
 AIDEQFGSLDELIK_2_Frag3_1,
 AIDEQFGSLDELIK_2_Frag4_1,
 AIDEQFGSLDELIK_2_Frag6_1,
 AIGVLPQLIIDR_3_Frag1_1,
 AIGVLPQLIIDR_3_Frag2_1,
 AIGVLPQLIIDR_3_Frag3_1,
 AIGVLPQLIIDR_3_Frag4_1,
 AIGVLPQLIIDR_3_Frag5_1,
 AIGVLPQLIIDR_3_Frag6_1,
 ALSADLAAR_2_Frag1_1,
 ALSADLAAR_2_Frag2_1,
 ANELLINVK_1_Frag1_1,
 ANELLINVK_1_Frag2_1,
 ASEEGNWSK_2_Frag1_1,
 ASEEGNWSK_2_Frag2_1,
 ASEEGNWSK_2_Frag3_1,
 ASEEGNWSK_2_Frag4_1,
 ASEEGNWSK_2_Frag5_1,
 ASEEGNWSK_2_Frag6_1,
 ATLTDLPER_2_Frag1_1,
 ATLTDLPER_2_Frag2_1,
 ATLTDLPER_2_Frag4_1,
 AVFNLASK_2_Frag1_1,
 AVFNLASK_2_Frag2_1,
 AVFNLASK_2_Frag3_1,
 AVFNLASK_2_Frag4_1,
 AVFNLASK_2_Frag5_1,
 AVFNLASK_2_Frag6_1,
 AVMC(UniMod:4)VAK_1_Frag1_1,
 AVMC(UniMod:4)VAK_1_Frag2_1,
 AVMC(UniMod:4)VAK_1_Frag3_1,
 AVMC(UniMod:4)VAK_1_Frag4_1,
 AVMC(UniMod:4)VAK_1_Frag5_1,
 AVMC(UniMod:4)VAK_1_Frag6_1,
 AYLDELK_2_Frag1_1,
 AYLDELK_2_Frag2_1,
 AYLDELK_2_Frag3_1,
 AYLDELK_2_Frag4_1,
 AYLDELK_2_Frag5_1,
 AYLDELK_2_Frag6_1,
 C(UniMod:4)DLGITGVDQVR_2_Frag1_1,
 C(UniMod:4)DLGITGVDQVR_2_Frag2_1,
 C(UniMod:4)DLGITGVDQVR_2_Frag3_1,
 C(UniMod:4)GALLDPFELINPR_2_Frag1_1,
 C(UniMod:4)GALLDPFELINPR_2_Frag3_1,
 C(UniMod:4)GALLDPFELINPR_2_Frag4_1,
 C(UniMod:4)GALLDPFELINPR_2_Frag5_1,
 DLQENLLVLR_2_Frag2_1,
 DLQENLLVLR_2_Frag3_1,
 DLQENLLVLR_2_Frag6_1
INFO  [2025-10-23 02:24:12] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:12] ** 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  [2025-10-23 02:24:12] ** Raw data from DIANN imported successfully.
INFO  [2025-10-23 02:24:12] ** Raw data from DIANN cleaned successfully.
INFO  [2025-10-23 02:24:12] ** Using provided annotation.
INFO  [2025-10-23 02:24:12] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:12] ** Filtering on Global Q Value < 0.01
INFO  [2025-10-23 02:24:12] ** MBR was not used to analyze the data. Now setting names and filtering
INFO  [2025-10-23 02:24:12] -- Filtering on GlobalPGQValue < 0.01
INFO  [2025-10-23 02:24:12] -- Filtering on GlobalQValue < 0.01
INFO  [2025-10-23 02:24:12] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:12] ** Sequences containing DECOY, Decoys are removed.
INFO  [2025-10-23 02:24:12] ** Sequences containing \(UniMod\:35\) are removed.
INFO  [2025-10-23 02:24:12] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:12] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:12] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:12] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:12] Proteins with a single feature are removed.
INFO  [2025-10-23 02:24:12] ** Run annotation merged with quantification data.
WARN  [2025-10-23 02:24:12] The following features have missing values in at least one run. MKWVTFISLLFLFSSAYSRG_4_Frag1_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag2_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag3_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag4_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag5_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag6_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag7_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag8_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag9_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag10_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag11_1,
 MKWVTFISLLFLFSSAYSRG_4_Frag12_1
INFO  [2025-10-23 02:24:12] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:12] ** 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 0.5s

test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    
test_converters_DIAUmpiretoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:12] ** Raw data from DIAUmpire imported successfully.
INFO  [2025-10-23 02:24:12] ** Using selected fragments and peptides.
INFO  [2025-10-23 02:24:12] ** Extracted the data from selected fragments and/or peptides.
INFO  [2025-10-23 02:24:12] ** Raw data from DIAUmpire cleaned successfully.
INFO  [2025-10-23 02:24:12] ** Using provided annotation.
INFO  [2025-10-23 02:24:12] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:12] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, FragmentIon
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:12] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:12] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:12] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:12] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:12] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:12] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:12] ** Fractionation handled.
INFO  [2025-10-23 02:24:12] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:12] ** 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 79ms

test_converters_FragPipetoMSstatsFormat.R    0 tests    
test_converters_FragPipetoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:12] ** Raw data from FragPipe imported successfully.
INFO  [2025-10-23 02:24:12] ** Using annotation extracted from quantification data.
INFO  [2025-10-23 02:24:12] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:12] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:12] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:12] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:12] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:12] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:12] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:12] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:12] ** Fractionation handled.
INFO  [2025-10-23 02:24:12] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:12] ** 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 48ms

test_converters_MaxQtoMSstatsFormat.R    0 tests    
test_converters_MaxQtoMSstatsFormat.R    0 tests    
test_converters_MaxQtoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:12] ** Raw data from MaxQuant imported successfully.
INFO  [2025-10-23 02:24:12] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:12] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:12] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-10-23 02:24:12] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-10-23 02:24:12] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2025-10-23 02:24:12] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2025-10-23 02:24:13] ** Raw data from MaxQuant cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using provided annotation.
INFO  [2025-10-23 02:24:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:13] ** 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 84ms

test_converters_MetamorpheusToMSstatsFormat.R    0 tests    
test_converters_MetamorpheusToMSstatsFormat.R    0 tests    
test_converters_MetamorpheusToMSstatsFormat.R    0 tests    
test_converters_MetamorpheusToMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:13] ** Raw data from Metamorpheus imported successfully.
INFO  [2025-10-23 02:24:13] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using provided annotation.
INFO  [2025-10-23 02:24:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:13] ** 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 46ms

test_converters_OpenMStoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:13] ** Raw data from OpenMS imported successfully.
INFO  [2025-10-23 02:24:13] ** Raw data from OpenMS cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using annotation extracted from quantification data.
INFO  [2025-10-23 02:24:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:13] ** 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 91ms

test_converters_OpenSWATHtoMSstatsFormat.R    0 tests    
test_converters_OpenSWATHtoMSstatsFormat.R    0 tests    
test_converters_OpenSWATHtoMSstatsFormat.R    0 tests    
test_converters_OpenSWATHtoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:13] ** Raw data from OpenSWATH imported successfully.
INFO  [2025-10-23 02:24:13] ** Raw data from OpenSWATH cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using provided annotation.
INFO  [2025-10-23 02:24:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:13] ** Rows with values of decoy equal to 1 are removed 
INFO  [2025-10-23 02:24:13] ** Rows with values not smaller than 0.01 in m_score are removed 
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:13] ** 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 77ms

test_converters_PDtoMSstatsFormat.R    0 tests    
test_converters_PDtoMSstatsFormat.R    0 tests    
test_converters_PDtoMSstatsFormat.R    0 tests    
test_converters_PDtoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:13] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-10-23 02:24:13] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using provided annotation.
INFO  [2025-10-23 02:24:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:13] ** 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 56ms

test_converters_ProgenesistoMSstatsFormat.R    0 tests    
test_converters_ProgenesistoMSstatsFormat.R    0 tests    
test_converters_ProgenesistoMSstatsFormat.R    0 tests    
test_converters_ProgenesistoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:13] ** Raw data from Progenesis imported successfully.
INFO  [2025-10-23 02:24:13] ** Raw data from Progenesis cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using provided annotation.
INFO  [2025-10-23 02:24:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:13] ** 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 57ms

test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    
test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    
test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    
test_converters_ProteinProspectortoMSstatsTMTFormat.R    0 tests    INFO  [2025-10-23 02:24:13] ** Raw data from ProteinProspector imported successfully.
INFO  [2025-10-23 02:24:13] ** Raw data from ProteinProspector cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using provided annotation.
INFO  [2025-10-23 02:24:13] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements within each run will be removed.
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-10-23 02:24:13] ** PSMs have been aggregated to peptide ions.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** For peptides overlapped between fractions of Mixture1_1 use the fraction with maximal average abundance.
INFO  [2025-10-23 02:24:13] ** Fractions belonging to same mixture have been combined.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:13] ** 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 0.2s

test_converters_SkylinetoMSstatsFormat.R    0 tests    
test_converters_SkylinetoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:13] ** Raw data from Skyline imported successfully.
INFO  [2025-10-23 02:24:13] ** Raw data from Skyline cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using annotation extracted from quantification data.
INFO  [2025-10-23 02:24:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:13] ** Rows with values of StandardType equal to iRT are removed 
INFO  [2025-10-23 02:24:13] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN  [2025-10-23 02:24:13] ** DetectionQValue not found in input columns.
INFO  [2025-10-23 02:24:13] ** Sequences containing DECOY, Decoys are removed.
INFO  [2025-10-23 02:24:13] ** Three isotopic preaks per feature and run are summed
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:13] ** 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 77ms

test_converters_SpectronauttoMSstatsFormat.R    0 tests    
test_converters_SpectronauttoMSstatsFormat.R    0 tests    INFO  [2025-10-23 02:24:13] ** Raw data from Spectronaut imported successfully.
INFO  [2025-10-23 02:24:13] ** Raw data from Spectronaut cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using annotation extracted from quantification data.
INFO  [2025-10-23 02:24:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:13] ** Intensities with values of FExcludedFromQuantification equal to TRUE are replaced with NA
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:13] ** 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   13 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   13 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   13 tests OK INFO  [2025-10-23 02:24:13] ** Raw data from Spectronaut imported successfully.

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 INFO  [2025-10-23 02:24:13] ** Raw data from Spectronaut imported successfully.

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 INFO  [2025-10-23 02:24:13] ** Raw data from Spectronaut imported successfully.

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 INFO  [2025-10-23 02:24:13] ** Raw data from Spectronaut imported successfully.

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 
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 
test_converters_SpectronauttoMSstatsFormat.R   17 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   17 tests OK INFO  [2025-10-23 02:24:13] ** Raw data from Spectronaut imported successfully.
INFO  [2025-10-23 02:24:13] ** Raw data from Spectronaut cleaned successfully.
INFO  [2025-10-23 02:24:13] ** Using annotation extracted from quantification data.
INFO  [2025-10-23 02:24:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-10-23 02:24:13] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:13] ** Intensities with values of FExcludedFromQuantification equal to TRUE are replaced with NA
INFO  [2025-10-23 02:24:13] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:13] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Run annotation merged with quantification data.
INFO  [2025-10-23 02:24:13] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:13] ** Fractionation handled.
INFO  [2025-10-23 02:24:13] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-23 02:24:14] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters_SpectronauttoMSstatsFormat.R   17 tests OK 
test_converters_SpectronauttoMSstatsFormat.R   18 tests OK 
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 0.8s

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 20ms

test_feature_cleaning.R.......    0 tests    
test_feature_cleaning.R.......    0 tests    
test_feature_cleaning.R.......    0 tests    
test_feature_cleaning.R.......    0 tests    INFO  [2025-10-23 02:24:14] ** Features with one or two measurements across channels within each run are removed.

test_feature_cleaning.R.......    1 tests OK INFO  [2025-10-23 02:24:14] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    2 tests OK INFO  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** Features with all missing measurements across runs are removed.

test_feature_cleaning.R.......    4 tests OK INFO  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests OK INFO  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] Proteins with a single feature are removed.

test_feature_cleaning.R.......   19 tests OK 
test_feature_cleaning.R.......   20 tests OK INFO  [2025-10-23 02:24:14] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:14] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......   20 tests OK INFO  [2025-10-23 02:24:14] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** Sequences containing \+ are removed.

test_filtering.R..............    2 tests OK INFO  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** Rows with values of Symbol_1 equal to - are removed 

test_filtering.R..............    7 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values of Symbol_1 equal to +, - are removed 

test_filtering.R..............    8 tests OK INFO  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** Rows with values of Symbol_1 equal to R are removed 

test_filtering.R..............   12 tests OK 
test_filtering.R..............   13 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2025-10-23 02:24:14] ** Rows with values of Symbol_2 equal to + are removed 

test_filtering.R..............   14 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   19 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   20 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   21 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   22 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   23 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   24 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   25 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   26 tests OK INFO  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** 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  [2025-10-23 02:24:14] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2025-10-23 02:24:14] ** Sequences containing \+ are removed.

test_filtering.R..............   36 tests OK INFO  [2025-10-23 02:24:14] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2025-10-23 02:24:14] ** Sequences containing \+ are removed.

test_filtering.R..............   37 tests OK 40ms

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..............    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 INFO  [2025-10-23 02:24:14] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2025-10-23 02:24:14] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2025-10-23 02:24:14] ** For peptides overlapped between fractions of 2_1 use the fraction with maximal average abundance.

test_fractions.R..............    8 tests OK 
test_fractions.R..............    9 tests OK 67ms

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  [2025-10-23 02:24:14] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2025-10-23 02:24:14] ** 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 11ms

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: 14 20 15 13 8 

test_utils_anomaly_score.R....   14 tests OK Score range: 0.2308879 0.5859702 

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 6.5s

test_utils_data_health.R......    0 tests    
test_utils_data_health.R......    0 tests    INFO  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 0% of the values are missing across all intensities
INFO  [2025-10-23 02:24:21] Intensity distribution standard truncated data.
INFO  [2025-10-23 02:24:21] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-10-23 02:24:21] 0% of all measured intensities fall within the outlier range
INFO  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 0% of the values are missing across all intensities
INFO  [2025-10-23 02:24:21] Intensity distribution standard truncated data.
INFO  [2025-10-23 02:24:21] 0% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-10-23 02:24:21] 0% of all measured intensities fall within the outlier range
INFO  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 0% of the values are missing across all intensities
INFO  [2025-10-23 02:24:21] Intensity distribution standard truncated data.
INFO  [2025-10-23 02:24:21] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-10-23 02:24:21] 0% of all measured intensities fall within the outlier range
INFO  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 0% of the values are missing across all intensities
INFO  [2025-10-23 02:24:21] Intensity distribution standard truncated data.
INFO  [2025-10-23 02:24:21] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-10-23 02:24:21] 0% of all measured intensities fall within the outlier range
INFO  [2025-10-23 02:24:21] 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  [2025-10-23 02:24:21] 0% of the values are missing across all intensities
INFO  [2025-10-23 02:24:21] Intensity distribution standard truncated data.
INFO  [2025-10-23 02:24:21] 20% of features have a ratio of standard deviation to mean > 0.5. A high value here could indicate problematic measurements.
INFO  [2025-10-23 02:24:21] 0% of all measured intensities fall within the outlier range
INFO  [2025-10-23 02:24:21] 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 0.1s

test_workflow.R...............    0 tests    
test_workflow.R...............    0 tests    INFO  [2025-10-23 02:24:21] ** Raw data from OpenMS imported successfully.

test_workflow.R...............    0 tests    
test_workflow.R...............    1 tests OK INFO  [2025-10-23 02:24:21] ** Raw data from OpenMS cleaned successfully.

test_workflow.R...............    1 tests OK 
test_workflow.R...............    2 tests OK INFO  [2025-10-23 02:24:21] ** Using annotation extracted from quantification data.
INFO  [2025-10-23 02:24:21] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_workflow.R...............    2 tests OK 
test_workflow.R...............    3 tests OK INFO  [2025-10-23 02:24:21] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-10-23 02:24:21] ** Features with all missing measurements across runs are removed.
INFO  [2025-10-23 02:24:21] ** Shared peptides are removed.
INFO  [2025-10-23 02:24:21] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-10-23 02:24:21] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:21] Proteins with a single feature are removed.
INFO  [2025-10-23 02:24:21] ** 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  [2025-10-23 02:24:21] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-23 02:24:21] ** Fractionation handled.
INFO  [2025-10-23 02:24:21] ** 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 56ms
All ok, 497 results (10.3s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> 
> proc.time()
   user  system elapsed 
  4.403   0.211  10.791

Example timings

MSstatsConvert.Rcheck/MSstatsConvert-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsFormat0.6900.0450.718
DIAUmpiretoMSstatsFormat0.0890.0010.078
FragPipetoMSstatsFormat0.0530.0010.043
MSstatsBalancedDesign0.0170.0000.017
MSstatsClean0.1010.0000.086
MSstatsImport0.0790.0040.078
MSstatsLogsSettings0.0130.0000.013
MSstatsMakeAnnotation0.1350.0030.122
MSstatsPreprocess0.1470.0000.105
MSstatsSaveSessionInfo0.0180.0100.108
MaxQtoMSstatsFormat0.1790.0020.105
MetamorpheusToMSstatsFormat0.0710.0010.060
OpenMStoMSstatsFormat0.0670.0000.056
OpenSWATHtoMSstatsFormat0.0820.0020.075
PDtoMSstatsFormat0.0790.0010.070
ProgenesistoMSstatsFormat0.0840.0010.074
ProteinProspectortoMSstatsTMTFormat0.2890.0030.281
SkylinetoMSstatsFormat0.1160.0030.098
SpectronauttoMSstatsFormat0.0730.0010.064
getDataType0.0690.0000.069
getInputFile0.0800.0010.081