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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1352/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsConvert 1.16.0  (landing page)
Mateusz Staniak
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/MSstatsConvert
git_branch: RELEASE_3_20
git_last_commit: 0ee36b7
git_last_commit_date: 2024-10-29 10:53:13 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for MSstatsConvert on lconway

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: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsConvert_1.16.0.tar.gz
StartedAt: 2024-11-20 00:23:56 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 00:28:14 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 257.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MSstatsConvert.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsConvert_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsConvert.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK
* this is package ‘MSstatsConvert’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  Warning: MSstatsConvert.Rd:3: docType ‘_PACKAGE’ is unrecognized
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsConvert.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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
.cleanRawDIANN: no visible binding for global variable ‘PrecursorMz’
.cleanRawDIANN: no visible binding for global variable ‘FragmentInfo’
.cleanRawDIANN: no visible binding for global variable ‘FragmentIon’
.cleanRawDIANN: no visible binding for global variable ‘ProductCharge’
.cleanRawDIANN: no visible binding for global variable
  ‘PeptideSequence’
.cleanRawPhilosopher: no visible binding for global variable ‘Run’
.summarizeMultiplePSMs: no visible binding for global variable ‘Purity’
.summarizeMultiplePSMs: no visible binding for global variable
  ‘PeptideProphet.Probability’
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’
SkylinetoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
SpectronauttoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘PrecursorMz’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘FragmentInfo’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘FragmentIon’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘ProductCharge’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘PeptideSequence’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘Run’
Undefined global functions or variables:
  DetectionQValue FragmentInfo FragmentIon GlobalPGQValue GlobalQValue
  Intensity LibPGQValue LibQValue PeptideProphet.Probability
  PeptideSequence PrecursorMz ProductCharge Purity Run
* checking Rd files ... WARNING
prepare_Rd: MSstatsConvert.Rd:3: docType ‘_PACKAGE’ is unrecognized
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'dot-cleanRawPDTMT.Rd':
.cleanRawPDTMT
  Code: function(msstats_object, remove_shared = TRUE,
                 remove_protein_groups = TRUE, protein_id_column =
                 "ProteinAccessions", intensity_columns_regexp =
                 "Abundance", run_column = "SpectrumFile")
  Docs: function(msstats_object, remove_shared = TRUE,
                 remove_protein_groups = TRUE, protein_id_column =
                 "ProteinAccessions", intensity_columns_regexp =
                 "Abundance")
  Argument names in code not in docs:
    run_column

Codoc mismatches from Rd file 'dot-validatePDTMTInputColumns.Rd':
.validatePDTMTInputColumns
  Code: function(pd_input, protein_id_column, num_proteins_column,
                 run_column, channels)
  Docs: function(pd_input, protein_id_column, num_proteins_column,
                 channels)
  Argument names in code not in docs:
    run_column
  Mismatches in argument names:
    Position: 4 Code: run_column Docs: channels

* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'dot-filterByPattern.Rd':
  ‘pattern’

Documented arguments not in \usage in Rd file 'dot-filterFewMeasurements.Rd':
  ‘features_columns’

Documented arguments not in \usage in Rd file 'dot-getFullDesign.Rd':
  ‘`feature_column`’ ‘`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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsConvert.Rcheck/00check.log’
for details.

Installation output

MSstatsConvert.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘MSstatsConvert’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: MSstatsConvert.Rd:3: docType ‘_PACKAGE’ is unrecognized
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsConvert)

Tests output

MSstatsConvert.Rcheck/tests/tinytest.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> 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 59ms

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  [2024-11-20 00:28:03] ** Using annotation extracted from quantification data.
INFO  [2024-11-20 00:28:03] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    1 tests OK INFO  [2024-11-20 00:28:03] ** Using provided annotation.
INFO  [2024-11-20 00:28:03] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    2 tests OK 
test_annotation.R.............    2 tests OK INFO  [2024-11-20 00:28:03] ** Using provided annotation.
INFO  [2024-11-20 00:28:03] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    3 tests OK INFO  [2024-11-20 00:28:03] ** Using provided annotation.
INFO  [2024-11-20 00:28:03] ** 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  [2024-11-20 00:28:03] ** Run annotation merged with quantification data.

test_annotation.R.............    6 tests OK INFO  [2024-11-20 00:28:03] ** Using provided annotation.
INFO  [2024-11-20 00:28:03] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    6 tests OK INFO  [2024-11-20 00:28:03] ** Run annotation merged with quantification data.

test_annotation.R.............    7 tests OK INFO  [2024-11-20 00:28:03] ** Using provided annotation.
INFO  [2024-11-20 00:28:03] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    7 tests OK 
test_annotation.R.............    8 tests OK INFO  [2024-11-20 00:28:03] ** Using provided annotation.
INFO  [2024-11-20 00:28:03] ** 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  [2024-11-20 00:28:03] ** 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 83ms

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2024-11-20 00:28:03] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2024-11-20 00:28:03] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2024-11-20 00:28:03] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2024-11-20 00:28:03] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2024-11-20 00:28:03] ** Using selected fragments and peptides.
INFO  [2024-11-20 00:28:03] ** Extracted the data from selected fragments and/or peptides.
INFO  [2024-11-20 00:28:03] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2024-11-20 00:28:03] ** Using selected fragments and peptides.
INFO  [2024-11-20 00:28:03] ** Extracted the data from selected fragments and/or peptides.
INFO  [2024-11-20 00:28:03] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2024-11-20 00:28:03] ** Using selected fragments.
INFO  [2024-11-20 00:28:03] ** Extracted the data from selected fragments and/or peptides.
INFO  [2024-11-20 00:28:03] ** 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  [2024-11-20 00:28:04] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2024-11-20 00:28:04] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2024-11-20 00:28:04] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............   13 tests OK INFO  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2024-11-20 00:28:04] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   15 tests OK 
test_cleanRaw.R...............   16 tests OK INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   18 tests OK INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Raw data from OpenSWATH imported successfully.

test_cleanRaw.R...............   20 tests OK INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK 
test_cleanRaw.R...............   30 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   37 tests OK 
test_cleanRaw.R...............   37 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2024-11-20 00:28:04] ** 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 [2024-11-20 00:28:04] 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 
test_cleanRaw.R...............   40 tests OK 
test_cleanRaw.R...............   40 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from Spectronaut cleaned successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2024-11-20 00:28:04] ** 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...............   43 tests OK 
test_cleanRaw.R...............   43 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from Metamorpheus imported successfully.

test_cleanRaw.R...............   43 tests OK 
test_cleanRaw.R...............   44 tests OK 0.6s

test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............    0 tests    INFO  [2024-11-20 00:28:04] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............    0 tests    
test_clean_DIANN.R............   15 tests OK INFO  [2024-11-20 00:28:04] ** Raw data from DIANN cleaned successfully.

test_clean_DIANN.R............   15 tests OK 
test_clean_DIANN.R............   30 tests OK 40ms

test_clean_Metamorpheus.R.....    0 tests    
test_clean_Metamorpheus.R.....    0 tests    INFO  [2024-11-20 00:28:04] ** Raw data from Metamorpheus cleaned successfully.

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

test_clean_ProteinProspector.R    0 tests    
test_clean_ProteinProspector.R    0 tests    
test_clean_ProteinProspector.R    0 tests    INFO  [2024-11-20 00:28:04] ** Raw data from ProteinProspector cleaned successfully.

test_clean_ProteinProspector.R    3 tests OK 7ms

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  [2024-11-20 00:28:04] ** Raw data from DIANN imported successfully.
INFO  [2024-11-20 00:28:04] ** Raw data from DIANN cleaned successfully.
INFO  [2024-11-20 00:28:04] ** Using provided annotation.
INFO  [2024-11-20 00:28:04] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:04] ** Filtering on Global Q Value < 0.01
INFO  [2024-11-20 00:28:04] ** MBR was not used to analyze the data. Now setting names and filtering
INFO  [2024-11-20 00:28:04] -- Filtering on GlobalPGQValue < 0.01
INFO  [2024-11-20 00:28:04] -- Filtering on GlobalQValue < 0.01
INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Sequences containing DECOY, Decoys are removed.
INFO  [2024-11-20 00:28:04] ** Sequences containing \(UniMod\:35\) are removed.
INFO  [2024-11-20 00:28:04] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:04] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] Proteins with a single feature are removed.
INFO  [2024-11-20 00:28:04] ** Run annotation merged with quantification data.
WARN  [2024-11-20 00:28:04] 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  [2024-11-20 00:28:04] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:04] ** 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 46ms

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  [2024-11-20 00:28:04] ** Raw data from DIAUmpire imported successfully.
INFO  [2024-11-20 00:28:04] ** Using selected fragments and peptides.
INFO  [2024-11-20 00:28:04] ** Extracted the data from selected fragments and/or peptides.
INFO  [2024-11-20 00:28:04] ** Raw data from DIAUmpire cleaned successfully.
INFO  [2024-11-20 00:28:04] ** Using provided annotation.
INFO  [2024-11-20 00:28:04] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:04] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Fractionation handled.
INFO  [2024-11-20 00:28:04] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:04] ** 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 67ms

test_converters_FragPipetoMSstatsFormat.R    0 tests    
test_converters_FragPipetoMSstatsFormat.R    0 tests    INFO  [2024-11-20 00:28:04] ** Raw data from FragPipe imported successfully.
INFO  [2024-11-20 00:28:04] ** Using annotation extracted from quantification data.
INFO  [2024-11-20 00:28:04] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:04] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Fractionation handled.
INFO  [2024-11-20 00:28:04] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:04] ** 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 43ms

test_converters_MaxQtoMSstatsFormat.R    0 tests    
test_converters_MaxQtoMSstatsFormat.R    0 tests    
test_converters_MaxQtoMSstatsFormat.R    0 tests    INFO  [2024-11-20 00:28:04] ** Raw data from MaxQuant imported successfully.
INFO  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-11-20 00:28:04] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2024-11-20 00:28:04] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2024-11-20 00:28:04] ** Raw data from MaxQuant cleaned successfully.
INFO  [2024-11-20 00:28:04] ** Using provided annotation.
INFO  [2024-11-20 00:28:04] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:04] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Fractionation handled.
INFO  [2024-11-20 00:28:04] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:04] ** 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 72ms

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  [2024-11-20 00:28:04] ** Raw data from Metamorpheus imported successfully.
INFO  [2024-11-20 00:28:04] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2024-11-20 00:28:04] ** Using provided annotation.
INFO  [2024-11-20 00:28:04] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:04] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Fractionation handled.
INFO  [2024-11-20 00:28:04] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:04] ** 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 48ms

test_converters_OpenMStoMSstatsFormat.R    0 tests    INFO  [2024-11-20 00:28:04] ** Raw data from OpenMS imported successfully.
INFO  [2024-11-20 00:28:04] ** Raw data from OpenMS cleaned successfully.
INFO  [2024-11-20 00:28:04] ** Using annotation extracted from quantification data.
INFO  [2024-11-20 00:28:04] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:04] ** 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  [2024-11-20 00:28:04] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:04] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:04] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:04] ** Fractionation handled.
INFO  [2024-11-20 00:28:04] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:04] ** 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 46ms

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  [2024-11-20 00:28:05] ** Raw data from OpenSWATH imported successfully.
INFO  [2024-11-20 00:28:05] ** Raw data from OpenSWATH cleaned successfully.
INFO  [2024-11-20 00:28:05] ** Using provided annotation.
INFO  [2024-11-20 00:28:05] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Rows with values of decoy equal to 1 are removed 
INFO  [2024-11-20 00:28:05] ** Rows with values not smaller than 0.01 in m_score are removed 
INFO  [2024-11-20 00:28:05] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:05] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Fractionation handled.
INFO  [2024-11-20 00:28:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:05] ** 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 59ms

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  [2024-11-20 00:28:05] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-11-20 00:28:05] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-11-20 00:28:05] ** Using provided annotation.
INFO  [2024-11-20 00:28:05] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:05] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Fractionation handled.
INFO  [2024-11-20 00:28:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:05] ** 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 47ms

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  [2024-11-20 00:28:05] ** Raw data from Progenesis imported successfully.
INFO  [2024-11-20 00:28:05] ** Raw data from Progenesis cleaned successfully.
INFO  [2024-11-20 00:28:05] ** Using provided annotation.
INFO  [2024-11-20 00:28:05] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:05] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Fractionation handled.
INFO  [2024-11-20 00:28:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:05] ** 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 42ms

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  [2024-11-20 00:28:05] ** Raw data from ProteinProspector imported successfully.
INFO  [2024-11-20 00:28:05] ** Raw data from ProteinProspector cleaned successfully.
INFO  [2024-11-20 00:28:05] ** Using provided annotation.
INFO  [2024-11-20 00:28:05] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-11-20 00:28:05] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-11-20 00:28:05] ** PSMs have been aggregated to peptide ions.
INFO  [2024-11-20 00:28:05] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:05] ** For peptides overlapped between fractions of Mixture1_1 use the fraction with maximal average abundance.
INFO  [2024-11-20 00:28:05] ** Fractions belonging to same mixture have been combined.
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-11-20 00:28:05] ** Fractionation handled.
INFO  [2024-11-20 00:28:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:05] ** 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 0.1s

test_converters_SkylinetoMSstatsFormat.R    0 tests    
test_converters_SkylinetoMSstatsFormat.R    0 tests    INFO  [2024-11-20 00:28:05] ** Raw data from Skyline imported successfully.
INFO  [2024-11-20 00:28:05] ** Raw data from Skyline cleaned successfully.
INFO  [2024-11-20 00:28:05] ** Using annotation extracted from quantification data.
INFO  [2024-11-20 00:28:05] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Rows with values of StandardType equal to iRT are removed 
INFO  [2024-11-20 00:28:05] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN  [2024-11-20 00:28:05] ** DetectionQValue not found in input columns.
INFO  [2024-11-20 00:28:05] ** Sequences containing DECOY, Decoys are removed.
INFO  [2024-11-20 00:28:05] ** Three isotopic preaks per feature and run are summed
INFO  [2024-11-20 00:28:05] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:05] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Fractionation handled.
INFO  [2024-11-20 00:28:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:05] ** 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 66ms

test_converters_SpectronauttoMSstatsFormat.R    0 tests    
test_converters_SpectronauttoMSstatsFormat.R    0 tests    INFO  [2024-11-20 00:28:05] ** Raw data from Spectronaut imported successfully.
INFO  [2024-11-20 00:28:05] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-11-20 00:28:05] ** Using annotation extracted from quantification data.
INFO  [2024-11-20 00:28:05] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:05] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Run annotation merged with quantification data.
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Fractionation handled.
INFO  [2024-11-20 00:28:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-20 00:28:05] ** 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 39ms

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 8ms

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  [2024-11-20 00:28:05] ** Features with one or two measurements across channels within each run are removed.

test_feature_cleaning.R.......    1 tests OK INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    2 tests OK INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Features with all missing measurements across runs are removed.

test_feature_cleaning.R.......    4 tests OK INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests OK INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] Proteins with a single feature are removed.

test_feature_cleaning.R.......   19 tests OK 
test_feature_cleaning.R.......   20 tests OK INFO  [2024-11-20 00:28:05] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......   20 tests OK INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-11-20 00:28:05] ** 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 0.2s

test_filtering.R..............    0 tests    
test_filtering.R..............    0 tests    
test_filtering.R..............    1 tests OK INFO  [2024-11-20 00:28:05] ** Sequences containing \+ are removed.

test_filtering.R..............    2 tests OK INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Rows with values of Symbol_1 equal to - are removed 

test_filtering.R..............    7 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values of Symbol_1 equal to +, - are removed 

test_filtering.R..............    8 tests OK INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Rows with values of Symbol_1 equal to R are removed 

test_filtering.R..............   12 tests OK 
test_filtering.R..............   13 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2024-11-20 00:28:05] ** Rows with values of Symbol_2 equal to + are removed 

test_filtering.R..............   14 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   19 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   20 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   21 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   22 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   23 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   24 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   25 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   26 tests OK INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2024-11-20 00:28:05] ** Sequences containing \+ are removed.

test_filtering.R..............   36 tests OK INFO  [2024-11-20 00:28:05] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2024-11-20 00:28:05] ** Sequences containing \+ are removed.

test_filtering.R..............   37 tests OK 29ms

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  [2024-11-20 00:28:05] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2024-11-20 00:28:05] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2024-11-20 00:28:05] ** 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 50ms

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  [2024-11-20 00:28:05] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2024-11-20 00:28:05] ** 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 8ms

test_workflow.R...............    0 tests    
test_workflow.R...............    0 tests    INFO  [2024-11-20 00:28:05] ** Raw data from OpenMS imported successfully.

test_workflow.R...............    0 tests    
test_workflow.R...............    1 tests OK INFO  [2024-11-20 00:28:05] ** Raw data from OpenMS cleaned successfully.

test_workflow.R...............    1 tests OK 
test_workflow.R...............    2 tests OK INFO  [2024-11-20 00:28:05] ** Using annotation extracted from quantification data.
INFO  [2024-11-20 00:28:05] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_workflow.R...............    2 tests OK 
test_workflow.R...............    3 tests OK INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Features with all missing measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Shared peptides are removed.
INFO  [2024-11-20 00:28:05] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] Proteins with a single feature are removed.
INFO  [2024-11-20 00:28:05] ** 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  [2024-11-20 00:28:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-20 00:28:05] ** Fractionation handled.
INFO  [2024-11-20 00:28:05] ** 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 38ms
All ok, 371 results (2.1s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> 
> proc.time()
   user  system elapsed 
  2.287   0.220   2.539

Example timings

MSstatsConvert.Rcheck/MSstatsConvert-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsFormat0.0990.0130.113
DIAUmpiretoMSstatsFormat0.0680.0060.076
FragPipetoMSstatsFormat0.0760.0040.080
MSstatsBalancedDesign0.0130.0010.015
MSstatsClean0.0850.0040.089
MSstatsImport0.0880.0060.094
MSstatsLogsSettings0.0590.0010.060
MSstatsMakeAnnotation0.1100.0080.119
MSstatsPreprocess0.1000.0090.110
MSstatsSaveSessionInfo0.0080.0060.014
MaxQtoMSstatsFormat0.0970.0090.106
MetamorpheusToMSstatsFormat0.0400.0050.046
OpenMStoMSstatsFormat0.0440.0020.047
OpenSWATHtoMSstatsFormat0.0420.0030.046
PDtoMSstatsFormat0.0400.0030.044
ProgenesistoMSstatsFormat0.0470.0030.052
ProteinProspectortoMSstatsTMTFormat0.1350.0060.142
SkylinetoMSstatsFormat0.0570.0070.065
SpectronauttoMSstatsFormat0.0410.0020.045
getDataType0.0650.0020.068
getInputFile0.0750.0050.080