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CHECK report for MSstatsConvert on tokay1

This page was generated on 2021-05-06 12:32:23 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MSstatsConvert package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1166/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsConvert 1.0.0  (landing page)
Mateusz Staniak
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MSstatsConvert
Branch: RELEASE_3_12
Last Commit: 90d207a
Last Changed Date: 2020-10-27 12:04:14 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MSstatsConvert
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsConvert.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MSstatsConvert_1.0.0.tar.gz
StartedAt: 2021-05-06 04:53:10 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:53:57 -0400 (Thu, 06 May 2021)
EllapsedTime: 47.0 seconds
RetCode: 0
Status:   OK   
CheckDir: MSstatsConvert.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsConvert.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MSstatsConvert_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MSstatsConvert.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSstatsConvert/DESCRIPTION' ... OK
* this is package 'MSstatsConvert' version '1.0.0'
* 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 whether package 'MSstatsConvert' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'tinytest.R'
 OK
** running tests for arch 'x64' ...
  Running 'tinytest.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

MSstatsConvert.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MSstatsConvert_1.0.0.tar.gz && rm -rf MSstatsConvert.buildbin-libdir && mkdir MSstatsConvert.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstatsConvert.buildbin-libdir MSstatsConvert_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MSstatsConvert_1.0.0.zip && rm MSstatsConvert_1.0.0.tar.gz MSstatsConvert_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1  529k    1  5597    0     0   105k      0  0:00:05 --:--:--  0:00:05  105k
100  529k  100  529k    0     0  9207k      0 --:--:-- --:--:-- --:--:-- 9286k

install for i386

* installing *source* package 'MSstatsConvert' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSstatsConvert'
    finding HTML links ... done
    MSstatsBalancedDesign                   html  
    MSstatsClean                            html  
    MSstatsConvert                          html  
    MSstatsImport                           html  
    MSstatsInputFiles                       html  
    MSstatsLogsSettings                     html  
    MSstatsMakeAnnotation                   html  
    MSstatsPreprocess                       html  
    MSstatsSaveSessionInfo                  html  
    dot-MSstatsFormat                       html  
    dot-addFractions                        html  
    dot-adjustIntensities                   html  
    dot-aggregatePSMstoPeptideIons          html  
    dot-checkAnnotation                     html  
    dot-checkDDA                            html  
    dot-checkDuplicatedMeasurements         html  
    dot-checkMSstatsParams                  html  
    dot-checkMultiRun                       html  
    dot-checkOverlappedFeatures             html  
    dot-cleanByFeature                      html  
    dot-cleanRawDIAUmpire                   html  
    dot-cleanRawMaxQuant                    html  
    dot-cleanRawOpenMS                      html  
    dot-cleanRawOpenSWATH                   html  
    dot-cleanRawPD                          html  
    dot-cleanRawPDMSstats                   html  
    dot-cleanRawPDTMT                       html  
    dot-cleanRawProgenesis                  html  
    dot-cleanRawSkyline                     html  
    dot-cleanRawSpectroMineTMT              html  
    dot-cleanRawSpectronaut                 html  
    dot-countCommonFeatures                 html  
    dot-fillValues                          html  
    dot-filterByPattern                     html  
    dot-filterByScore                       html  
    dot-filterExact                         html  
    dot-filterFewMeasurements               html  
    dot-filterManyColumns                   html  
    dot-filterOverlapped                    html  
    dot-findAvailable                       html  
    dot-fixColumnTypes                      html  
    dot-fixMissingValues                    html  
    dot-getChannelColumns                   html  
    dot-getCorrectFraction                  html  
    dot-getDataTable                        html  
    dot-getFullDesign                       html  
    dot-getMissingRunsPerFeature            html  
    dot-getOverlappingFeatures              html  
    dot-handleFiltering                     html  
    dot-handleFractions                     html  
    dot-handleFractionsLF                   html  
    dot-handleFractionsTMT                  html  
    dot-handleIsotopicPeaks                 html  
    dot-handleSharedPeptides                html  
    dot-handleSingleFeaturePerProtein       html  
    dot-logConverterOptions                 html  
    dot-logSuccess                          html  
    dot-makeBalancedDesign                  html  
    dot-makeExactFilterMessage              html  
    dot-makeScoreFilterMessage              html  
    dot-mergeAnnotation                     html  
    dot-nullAppender                        html  
    dot-onLoad                              html  
    dot-removeOverlappingFeatures           html  
    dot-removeSharedPeptides                html  
    dot-selectMSstatsColumns                html  
    dot-standardizeColnames                 html  
    dot-summarizeMultipleMeasurements       html  
    dot-summarizeMultiplePSMs               html  
    getDataType                             html  
    getInputFile                            html  
** 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

install for x64

* installing *source* package 'MSstatsConvert' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstatsConvert' as MSstatsConvert_1.0.0.zip
* DONE (MSstatsConvert)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MSstatsConvert' successfully unpacked and MD5 sums checked

Tests output

MSstatsConvert.Rcheck/tests_i386/tinytest.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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")
+ }

Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    1 tests OK 
Running test_MSstatsConvert.R.........    2 tests OK 
Running test_MSstatsConvert.R.........    3 tests OK 
Running test_MSstatsConvert.R.........    4 tests OK 
Running test_MSstatsConvert.R.........    5 tests OK 
Running test_MSstatsConvert.R.........    6 tests OK 0.1s

Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    INFO  [2021-05-06 04:53:46] ** Using annotation extracted from quantification data.
INFO  [2021-05-06 04:53:46] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    1 tests OK INFO  [2021-05-06 04:53:46] ** Using provided annotation.
INFO  [2021-05-06 04:53:46] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    2 tests OK 
Running test_annotation.R.............    2 tests OK INFO  [2021-05-06 04:53:46] ** Using provided annotation.
INFO  [2021-05-06 04:53:46] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    3 tests OK INFO  [2021-05-06 04:53:46] ** Using provided annotation.
INFO  [2021-05-06 04:53:46] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    4 tests OK 
Running test_annotation.R.............    4 tests OK 
Running test_annotation.R.............    4 tests OK 
Running test_annotation.R.............    5 tests OK INFO  [2021-05-06 04:53:46] ** Run annotation merged with quantification data.

Running test_annotation.R.............    6 tests OK INFO  [2021-05-06 04:53:46] ** Using provided annotation.
INFO  [2021-05-06 04:53:46] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    6 tests OK INFO  [2021-05-06 04:53:46] ** Run annotation merged with quantification data.

Running test_annotation.R.............    7 tests OK INFO  [2021-05-06 04:53:46] ** Using provided annotation.
INFO  [2021-05-06 04:53:46] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    7 tests OK 
Running test_annotation.R.............    8 tests OK INFO  [2021-05-06 04:53:46] ** Using provided annotation.
INFO  [2021-05-06 04:53:46] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    8 tests OK 
Running test_annotation.R.............    9 tests OK 
Running test_annotation.R.............   10 tests OK INFO  [2021-05-06 04:53:46] ** Using provided annotation.

Running test_annotation.R.............   11 tests OK 47ms

Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    1 tests OK 
Running test_balanced_design.R........    2 tests OK 
Running test_balanced_design.R........    3 tests OK 
Running test_balanced_design.R........    3 tests OK 
Running test_balanced_design.R........    3 tests OK 
Running test_balanced_design.R........    3 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    5 tests OK 
Running test_balanced_design.R........    5 tests OK 
Running test_balanced_design.R........    6 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    8 tests OK 
Running test_balanced_design.R........    9 tests OK 
Running test_balanced_design.R........   10 tests OK 
Running test_balanced_design.R........   11 tests OK 0.2s

Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:47] ** Raw data from DIAUmpire imported successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:47] ** Raw data from DIAUmpire imported successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:47] ** Raw data from DIAUmpire imported successfully.

Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:47] ** Raw data from DIAUmpire imported successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:47] ** Using selected fragments and peptides.
INFO  [2021-05-06 04:53:47] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-05-06 04:53:47] ** Raw data from DIAUmpire cleaned successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:47] ** Using selected fragments and peptides.
INFO  [2021-05-06 04:53:47] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-05-06 04:53:47] ** Raw data from DIAUmpire cleaned successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:47] ** Using selected fragments.
INFO  [2021-05-06 04:53:47] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-05-06 04:53:47] ** Raw data from DIAUmpire cleaned successfully.

Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    1 tests OK 
Running test_cleanRaw.R...............    2 tests OK 
Running test_cleanRaw.R...............    3 tests OK 
Running test_cleanRaw.R...............    4 tests OK 
Running test_cleanRaw.R...............    5 tests OK 
Running test_cleanRaw.R...............    6 tests OK 
Running test_cleanRaw.R...............    7 tests OK 
Running test_cleanRaw.R...............    8 tests OK 
Running test_cleanRaw.R...............    9 tests OK 
Running test_cleanRaw.R...............    9 tests OK 
Running test_cleanRaw.R...............    9 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from MaxQuant imported successfully.

Running test_cleanRaw.R...............    9 tests OK INFO  [2021-05-06 04:53:47] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:47] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-05-06 04:53:47] ** Raw data from MaxQuant cleaned successfully.

Running test_cleanRaw.R...............    9 tests OK INFO  [2021-05-06 04:53:47] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2021-05-06 04:53:47] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2021-05-06 04:53:47] ** Raw data from MaxQuant cleaned successfully.

Running test_cleanRaw.R...............    9 tests OK 
Running test_cleanRaw.R...............   10 tests OK 
Running test_cleanRaw.R...............   11 tests OK INFO  [2021-05-06 04:53:47] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:47] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-05-06 04:53:47] ** Raw data from MaxQuant cleaned successfully.

Running test_cleanRaw.R...............   12 tests OK 
Running test_cleanRaw.R...............   13 tests OK 
Running test_cleanRaw.R...............   13 tests OK 
Running test_cleanRaw.R...............   13 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from MaxQuant imported successfully.

Running test_cleanRaw.R...............   13 tests OK INFO  [2021-05-06 04:53:47] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:47] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:47] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-05-06 04:53:47] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-05-06 04:53:47] ** Raw data from MaxQuant cleaned successfully.

Running test_cleanRaw.R...............   13 tests OK 
Running test_cleanRaw.R...............   14 tests OK 
Running test_cleanRaw.R...............   15 tests OK 
Running test_cleanRaw.R...............   15 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from OpenMS imported successfully.

Running test_cleanRaw.R...............   15 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from OpenMS imported successfully.

Running test_cleanRaw.R...............   15 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from OpenMS cleaned successfully.

Running test_cleanRaw.R...............   15 tests OK 
Running test_cleanRaw.R...............   16 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from OpenMS cleaned successfully.

Running test_cleanRaw.R...............   17 tests OK 
Running test_cleanRaw.R...............   18 tests OK 
Running test_cleanRaw.R...............   18 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from OpenMS imported successfully.

Running test_cleanRaw.R...............   18 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from OpenMS cleaned successfully.

Running test_cleanRaw.R...............   18 tests OK 
Running test_cleanRaw.R...............   19 tests OK 
Running test_cleanRaw.R...............   20 tests OK 
Running test_cleanRaw.R...............   20 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from OpenSWATH imported successfully.

Running test_cleanRaw.R...............   20 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from OpenSWATH cleaned successfully.

Running test_cleanRaw.R...............   20 tests OK 
Running test_cleanRaw.R...............   21 tests OK 
Running test_cleanRaw.R...............   22 tests OK 
Running test_cleanRaw.R...............   22 tests OK 
Running test_cleanRaw.R...............   22 tests OK 
Running test_cleanRaw.R...............   22 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   22 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   22 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   22 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   22 tests OK 
Running test_cleanRaw.R...............   23 tests OK 
Running test_cleanRaw.R...............   24 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:47] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   26 tests OK 
Running test_cleanRaw.R...............   27 tests OK 
Running test_cleanRaw.R...............   28 tests OK 
Running test_cleanRaw.R...............   29 tests OK 
Running test_cleanRaw.R...............   30 tests OK 
Running test_cleanRaw.R...............   30 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Progenesis imported successfully.

Running test_cleanRaw.R...............   30 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Progenesis imported successfully.

Running test_cleanRaw.R...............   30 tests OK 
Running test_cleanRaw.R...............   30 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Progenesis cleaned successfully.

Running test_cleanRaw.R...............   30 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Progenesis cleaned successfully.

Running test_cleanRaw.R...............   30 tests OK 
Running test_cleanRaw.R...............   31 tests OK 
Running test_cleanRaw.R...............   32 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Skyline imported successfully.

Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Skyline imported successfully.

Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Skyline imported successfully.

Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Skyline cleaned successfully.

Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Skyline cleaned successfully.

Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   34 tests OK 
Running test_cleanRaw.R...............   35 tests OK 
Running test_cleanRaw.R...............   36 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Skyline cleaned successfully.

Running test_cleanRaw.R...............   37 tests OK 
Running test_cleanRaw.R...............   37 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from SpectroMine imported successfully.

Running test_cleanRaw.R...............   37 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from SpectroMine imported successfully.

Running test_cleanRaw.R...............   37 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from SpectroMine cleaned successfully.

Running test_cleanRaw.R...............   37 tests OK 
Running test_cleanRaw.R...............   38 tests OK 
Running test_cleanRaw.R...............   39 tests OK ERROR [2021-05-06 04:53:48] There is no channel intensity column in the input data, which should start with 'PSM' and end with 'Raw'.

Running test_cleanRaw.R...............   40 tests OK 
Running test_cleanRaw.R...............   40 tests OK 
Running test_cleanRaw.R...............   40 tests OK 
Running test_cleanRaw.R...............   40 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Spectronaut imported successfully.

Running test_cleanRaw.R...............   40 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Spectronaut imported successfully.

Running test_cleanRaw.R...............   40 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Spectronaut cleaned successfully.

Running test_cleanRaw.R...............   40 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from Spectronaut cleaned successfully.

Running test_cleanRaw.R...............   40 tests OK 
Running test_cleanRaw.R...............   41 tests OK 
Running test_cleanRaw.R...............   42 tests OK 
Running test_cleanRaw.R...............   43 tests OK 1.2s

Running test_dt.R.....................    0 tests    
Running test_dt.R.....................    0 tests    
Running test_dt.R.....................    1 tests OK 
Running test_dt.R.....................    2 tests OK 
Running test_dt.R.....................    3 tests OK 
Running test_dt.R.....................    4 tests OK 
Running test_dt.R.....................    5 tests OK 
Running test_dt.R.....................    6 tests OK 
Running test_dt.R.....................    6 tests OK 
Running test_dt.R.....................    7 tests OK 
Running test_dt.R.....................    7 tests OK 
Running test_dt.R.....................    7 tests OK 
Running test_dt.R.....................    8 tests OK 
Running test_dt.R.....................    9 tests OK 
Running test_dt.R.....................   10 tests OK 16ms

Running test_feature_cleaning.R.......    0 tests    
Running test_feature_cleaning.R.......    0 tests    
Running test_feature_cleaning.R.......    0 tests    
Running test_feature_cleaning.R.......    0 tests    INFO  [2021-05-06 04:53:48] ** Features with one or two measurements across channels within each run are removed.

Running test_feature_cleaning.R.......    1 tests OK INFO  [2021-05-06 04:53:48] ** Features with one or two measurements across runs are removed.

Running test_feature_cleaning.R.......    2 tests OK INFO  [2021-05-06 04:53:48] ** Features with one or two measurements across runs are removed.

Running test_feature_cleaning.R.......    3 tests OK 
Running test_feature_cleaning.R.......    3 tests OK 
Running test_feature_cleaning.R.......    3 tests OK INFO  [2021-05-06 04:53:48] ** Features with all missing measurements across runs are removed.

Running test_feature_cleaning.R.......    4 tests OK INFO  [2021-05-06 04:53:48] ** Features with one or two measurements across runs are removed.

Running test_feature_cleaning.R.......    5 tests OK 
Running test_feature_cleaning.R.......    5 tests OK 
Running test_feature_cleaning.R.......    5 tests OK 
Running test_feature_cleaning.R.......    6 tests OK 
Running test_feature_cleaning.R.......    6 tests OK 
Running test_feature_cleaning.R.......    6 tests OK 
Running test_feature_cleaning.R.......    6 tests OK 
Running test_feature_cleaning.R.......    7 tests OK INFO  [2021-05-06 04:53:48] ** Three isotopic preaks per feature and run are summed

Running test_feature_cleaning.R.......    8 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......   10 tests OK 
Running test_feature_cleaning.R.......   10 tests OK 
Running test_feature_cleaning.R.......   10 tests OK 
Running test_feature_cleaning.R.......   11 tests OK 
Running test_feature_cleaning.R.......   11 tests OK 
Running test_feature_cleaning.R.......   11 tests OK 
Running test_feature_cleaning.R.......   12 tests OK 
Running test_feature_cleaning.R.......   12 tests OK 
Running test_feature_cleaning.R.......   13 tests OK 
Running test_feature_cleaning.R.......   13 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   15 tests OK 
Running test_feature_cleaning.R.......   15 tests OK INFO  [2021-05-06 04:53:48] ** PSMs have been aggregated to peptide ions.

Running test_feature_cleaning.R.......   16 tests OK INFO  [2021-05-06 04:53:48] ** PSMs have been aggregated to peptide ions.

Running test_feature_cleaning.R.......   16 tests OK 
Running test_feature_cleaning.R.......   17 tests OK 
Running test_feature_cleaning.R.......   17 tests OK 
Running test_feature_cleaning.R.......   17 tests OK 
Running test_feature_cleaning.R.......   18 tests OK INFO  [2021-05-06 04:53:48] Proteins with a single feature are removed.

Running test_feature_cleaning.R.......   19 tests OK 
Running test_feature_cleaning.R.......   20 tests OK INFO  [2021-05-06 04:53:48] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2021-05-06 04:53:48] ** Features with one or two measurements across runs are removed.

Running test_feature_cleaning.R.......   20 tests OK INFO  [2021-05-06 04:53:48] ** Features with one or two measurements across channels within each run are removed.
INFO  [2021-05-06 04:53:48] ** PSMs have been aggregated to peptide ions.

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

Running test_filtering.R..............    0 tests    
Running test_filtering.R..............    0 tests    
Running test_filtering.R..............    1 tests OK INFO  [2021-05-06 04:53:48] ** Sequences containing \+ are removed.

Running test_filtering.R..............    2 tests OK INFO  [2021-05-06 04:53:48] ** Sequences containing \+ are removed.

Running test_filtering.R..............    3 tests OK 
Running test_filtering.R..............    4 tests OK 
Running test_filtering.R..............    5 tests OK 
Running test_filtering.R..............    6 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_1 equal to - are removed 

Running test_filtering.R..............    7 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_1 equal to +, - are removed 

Running test_filtering.R..............    8 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_1 equal to + are removed 

Running test_filtering.R..............    9 tests OK 
Running test_filtering.R..............   10 tests OK 
Running test_filtering.R..............   11 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_1 equal to R are removed 

Running test_filtering.R..............   12 tests OK 
Running test_filtering.R..............   13 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_2 equal to + are removed 

Running test_filtering.R..............   14 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_2 equal to X are removed 

Running test_filtering.R..............   15 tests OK 
Running test_filtering.R..............   16 tests OK 
Running test_filtering.R..............   17 tests OK 
Running test_filtering.R..............   18 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values greater than 0.3 in Score are removed 

Running test_filtering.R..............   19 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values greater than 0.3 in Score are removed 

Running test_filtering.R..............   20 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values greater than 0.3 in Score are removed 

Running test_filtering.R..............   21 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values greater than 0.3 in Score are removed 

Running test_filtering.R..............   22 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values smaller than 0.3 in Score are removed 

Running test_filtering.R..............   23 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values smaller than 0.3 in Score are removed 

Running test_filtering.R..............   24 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values smaller than 0.3 in Score are removed 

Running test_filtering.R..............   25 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values smaller than 0.3 in Score are removed 

Running test_filtering.R..............   26 tests OK INFO  [2021-05-06 04:53:48] ** Intensities with values greater than 0.3 in Score are replaced with NA

Running test_filtering.R..............   26 tests OK 
Running test_filtering.R..............   27 tests OK 
Running test_filtering.R..............   28 tests OK INFO  [2021-05-06 04:53:48] ** Intensities with values greater than 0.3 in Score are replaced with NA

Running test_filtering.R..............   28 tests OK 
Running test_filtering.R..............   29 tests OK 
Running test_filtering.R..............   30 tests OK INFO  [2021-05-06 04:53:48] ** Intensities with values smaller than 0.3 in Score are replaced with NA

Running test_filtering.R..............   30 tests OK 
Running test_filtering.R..............   31 tests OK 
Running test_filtering.R..............   32 tests OK INFO  [2021-05-06 04:53:48] ** Intensities with values smaller than 0.3 in Score are replaced with NA

Running test_filtering.R..............   32 tests OK 
Running test_filtering.R..............   33 tests OK 
Running test_filtering.R..............   34 tests OK 
Running test_filtering.R..............   35 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-05-06 04:53:48] ** Sequences containing \+ are removed.

Running test_filtering.R..............   36 tests OK INFO  [2021-05-06 04:53:48] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-05-06 04:53:48] ** Sequences containing \+ are removed.

Running test_filtering.R..............   37 tests OK 31ms

Running test_fractions.R..............    0 tests    
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    2 tests OK 
Running test_fractions.R..............    3 tests OK 
Running test_fractions.R..............    4 tests OK 
Running test_fractions.R..............    4 tests OK 
Running test_fractions.R..............    5 tests OK 
Running test_fractions.R..............    5 tests OK 
Running test_fractions.R..............    5 tests OK 
Running test_fractions.R..............    5 tests OK 
Running test_fractions.R..............    6 tests OK 
Running test_fractions.R..............    7 tests OK 
Running test_fractions.R..............    8 tests OK 
Running test_fractions.R..............    8 tests OK INFO  [2021-05-06 04:53:48] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2021-05-06 04:53:48] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2021-05-06 04:53:48] ** For peptides overlapped between fractions of 2_1 use the fraction with maximal average abundance.

Running test_fractions.R..............    8 tests OK 
Running test_fractions.R..............    9 tests OK 62ms

Running test_logging.R................    1 tests OK 
Running test_logging.R................    2 tests OK 
Running test_logging.R................    3 tests OK 0ms

Running test_shared_peptides.R........    0 tests    
Running test_shared_peptides.R........    0 tests    INFO  [2021-05-06 04:53:48] ** Shared peptides are removed.

Running test_shared_peptides.R........    0 tests    
Running test_shared_peptides.R........    0 tests    INFO  [2021-05-06 04:53:48] ** Shared peptides are removed.

Running test_shared_peptides.R........    0 tests    
Running test_shared_peptides.R........    1 tests OK 
Running test_shared_peptides.R........    2 tests OK 
Running test_shared_peptides.R........    3 tests OK 
Running test_shared_peptides.R........    4 tests OK 
Running test_shared_peptides.R........    5 tests OK 16ms

Running test_workflow.R...............    0 tests    
Running test_workflow.R...............    0 tests    INFO  [2021-05-06 04:53:48] ** Raw data from OpenMS imported successfully.

Running test_workflow.R...............    0 tests    
Running test_workflow.R...............    1 tests OK INFO  [2021-05-06 04:53:48] ** Raw data from OpenMS cleaned successfully.

Running test_workflow.R...............    1 tests OK 
Running test_workflow.R...............    2 tests OK INFO  [2021-05-06 04:53:48] ** Using annotation extracted from quantification data.
INFO  [2021-05-06 04:53:48] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_workflow.R...............    2 tests OK 
Running test_workflow.R...............    3 tests OK INFO  [2021-05-06 04:53:48] ** 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  [2021-05-06 04:53:48] ** Features with all missing measurements across runs are removed.
INFO  [2021-05-06 04:53:48] ** Shared peptides are removed.
INFO  [2021-05-06 04:53:48] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2021-05-06 04:53:48] ** Features with one or two measurements across runs are removed.
INFO  [2021-05-06 04:53:48] Proteins with a single feature are removed.
INFO  [2021-05-06 04:53:48] ** Run annotation merged with quantification data.

Running test_workflow.R...............    3 tests OK 
Running test_workflow.R...............    4 tests OK 
Running test_workflow.R...............    5 tests OK 
Running test_workflow.R...............    6 tests OK INFO  [2021-05-06 04:53:48] ** Features with one or two measurements across runs are removed.
INFO  [2021-05-06 04:53:48] ** Fractionation handled.
INFO  [2021-05-06 04:53:48] ** Updated quantification data to make balanced design. Missing values are marked by NA

Running test_workflow.R...............    6 tests OK 
Running test_workflow.R...............    7 tests OK 
Running test_workflow.R...............    8 tests OK 62ms
All ok, 165 results (2.1s)
There were 29 warnings (use warnings() to see them)
> 
> 
> proc.time()
   user  system elapsed 
   1.90    0.18    2.59

MSstatsConvert.Rcheck/tests_x64/tinytest.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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")
+ }

Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    0 tests    
Running test_MSstatsConvert.R.........    1 tests OK 
Running test_MSstatsConvert.R.........    2 tests OK 
Running test_MSstatsConvert.R.........    3 tests OK 
Running test_MSstatsConvert.R.........    4 tests OK 
Running test_MSstatsConvert.R.........    5 tests OK 
Running test_MSstatsConvert.R.........    6 tests OK 0.2s

Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    
Running test_annotation.R.............    0 tests    INFO  [2021-05-06 04:53:50] ** Using annotation extracted from quantification data.
INFO  [2021-05-06 04:53:50] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    1 tests OK INFO  [2021-05-06 04:53:50] ** Using provided annotation.
INFO  [2021-05-06 04:53:50] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    2 tests OK 
Running test_annotation.R.............    2 tests OK INFO  [2021-05-06 04:53:50] ** Using provided annotation.
INFO  [2021-05-06 04:53:50] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    3 tests OK INFO  [2021-05-06 04:53:50] ** Using provided annotation.
INFO  [2021-05-06 04:53:50] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    4 tests OK 
Running test_annotation.R.............    4 tests OK 
Running test_annotation.R.............    4 tests OK 
Running test_annotation.R.............    5 tests OK INFO  [2021-05-06 04:53:50] ** Run annotation merged with quantification data.

Running test_annotation.R.............    6 tests OK INFO  [2021-05-06 04:53:50] ** Using provided annotation.
INFO  [2021-05-06 04:53:50] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    6 tests OK INFO  [2021-05-06 04:53:50] ** Run annotation merged with quantification data.

Running test_annotation.R.............    7 tests OK INFO  [2021-05-06 04:53:50] ** Using provided annotation.
INFO  [2021-05-06 04:53:50] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    7 tests OK 
Running test_annotation.R.............    8 tests OK INFO  [2021-05-06 04:53:50] ** Using provided annotation.
INFO  [2021-05-06 04:53:50] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

Running test_annotation.R.............    8 tests OK 
Running test_annotation.R.............    9 tests OK 
Running test_annotation.R.............   10 tests OK INFO  [2021-05-06 04:53:50] ** Using provided annotation.

Running test_annotation.R.............   11 tests OK 78ms

Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    0 tests    
Running test_balanced_design.R........    1 tests OK 
Running test_balanced_design.R........    2 tests OK 
Running test_balanced_design.R........    3 tests OK 
Running test_balanced_design.R........    3 tests OK 
Running test_balanced_design.R........    3 tests OK 
Running test_balanced_design.R........    3 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    4 tests OK 
Running test_balanced_design.R........    5 tests OK 
Running test_balanced_design.R........    5 tests OK 
Running test_balanced_design.R........    6 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    7 tests OK 
Running test_balanced_design.R........    8 tests OK 
Running test_balanced_design.R........    9 tests OK 
Running test_balanced_design.R........   10 tests OK 
Running test_balanced_design.R........   11 tests OK 0.1s

Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:50] ** Raw data from DIAUmpire imported successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:50] ** Raw data from DIAUmpire imported successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:50] ** Raw data from DIAUmpire imported successfully.

Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:50] ** Raw data from DIAUmpire imported successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:50] ** Using selected fragments and peptides.
INFO  [2021-05-06 04:53:50] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-05-06 04:53:50] ** Raw data from DIAUmpire cleaned successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:50] ** Using selected fragments and peptides.
INFO  [2021-05-06 04:53:50] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-05-06 04:53:50] ** Raw data from DIAUmpire cleaned successfully.

Running test_cleanRaw.R...............    0 tests    INFO  [2021-05-06 04:53:50] ** Using selected fragments.
INFO  [2021-05-06 04:53:50] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-05-06 04:53:50] ** Raw data from DIAUmpire cleaned successfully.

Running test_cleanRaw.R...............    0 tests    
Running test_cleanRaw.R...............    1 tests OK 
Running test_cleanRaw.R...............    2 tests OK 
Running test_cleanRaw.R...............    3 tests OK 
Running test_cleanRaw.R...............    4 tests OK 
Running test_cleanRaw.R...............    5 tests OK 
Running test_cleanRaw.R...............    6 tests OK 
Running test_cleanRaw.R...............    7 tests OK 
Running test_cleanRaw.R...............    8 tests OK 
Running test_cleanRaw.R...............    9 tests OK 
Running test_cleanRaw.R...............    9 tests OK 
Running test_cleanRaw.R...............    9 tests OK INFO  [2021-05-06 04:53:50] ** Raw data from MaxQuant imported successfully.

Running test_cleanRaw.R...............    9 tests OK INFO  [2021-05-06 04:53:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:50] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-05-06 04:53:50] ** Raw data from MaxQuant cleaned successfully.

Running test_cleanRaw.R...............    9 tests OK INFO  [2021-05-06 04:53:51] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2021-05-06 04:53:51] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2021-05-06 04:53:51] ** Raw data from MaxQuant cleaned successfully.

Running test_cleanRaw.R...............    9 tests OK 
Running test_cleanRaw.R...............   10 tests OK 
Running test_cleanRaw.R...............   11 tests OK INFO  [2021-05-06 04:53:51] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:51] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-05-06 04:53:51] ** Raw data from MaxQuant cleaned successfully.

Running test_cleanRaw.R...............   12 tests OK 
Running test_cleanRaw.R...............   13 tests OK 
Running test_cleanRaw.R...............   13 tests OK 
Running test_cleanRaw.R...............   13 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from MaxQuant imported successfully.

Running test_cleanRaw.R...............   13 tests OK INFO  [2021-05-06 04:53:51] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-05-06 04:53:51] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-05-06 04:53:51] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-05-06 04:53:51] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-05-06 04:53:51] ** Raw data from MaxQuant cleaned successfully.

Running test_cleanRaw.R...............   13 tests OK 
Running test_cleanRaw.R...............   14 tests OK 
Running test_cleanRaw.R...............   15 tests OK 
Running test_cleanRaw.R...............   15 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from OpenMS imported successfully.

Running test_cleanRaw.R...............   15 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from OpenMS imported successfully.

Running test_cleanRaw.R...............   15 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from OpenMS cleaned successfully.

Running test_cleanRaw.R...............   15 tests OK 
Running test_cleanRaw.R...............   16 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from OpenMS cleaned successfully.

Running test_cleanRaw.R...............   17 tests OK 
Running test_cleanRaw.R...............   18 tests OK 
Running test_cleanRaw.R...............   18 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from OpenMS imported successfully.

Running test_cleanRaw.R...............   18 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from OpenMS cleaned successfully.

Running test_cleanRaw.R...............   18 tests OK 
Running test_cleanRaw.R...............   19 tests OK 
Running test_cleanRaw.R...............   20 tests OK 
Running test_cleanRaw.R...............   20 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from OpenSWATH imported successfully.

Running test_cleanRaw.R...............   20 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from OpenSWATH cleaned successfully.

Running test_cleanRaw.R...............   20 tests OK 
Running test_cleanRaw.R...............   21 tests OK 
Running test_cleanRaw.R...............   22 tests OK 
Running test_cleanRaw.R...............   22 tests OK 
Running test_cleanRaw.R...............   22 tests OK 
Running test_cleanRaw.R...............   22 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   22 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   22 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   22 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   22 tests OK 
Running test_cleanRaw.R...............   23 tests OK 
Running test_cleanRaw.R...............   24 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer imported successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   25 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from ProteomeDiscoverer cleaned successfully.

Running test_cleanRaw.R...............   25 tests OK 
Running test_cleanRaw.R...............   26 tests OK 
Running test_cleanRaw.R...............   27 tests OK 
Running test_cleanRaw.R...............   28 tests OK 
Running test_cleanRaw.R...............   29 tests OK 
Running test_cleanRaw.R...............   30 tests OK 
Running test_cleanRaw.R...............   30 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Progenesis imported successfully.

Running test_cleanRaw.R...............   30 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Progenesis imported successfully.

Running test_cleanRaw.R...............   30 tests OK 
Running test_cleanRaw.R...............   30 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Progenesis cleaned successfully.

Running test_cleanRaw.R...............   30 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Progenesis cleaned successfully.

Running test_cleanRaw.R...............   30 tests OK 
Running test_cleanRaw.R...............   31 tests OK 
Running test_cleanRaw.R...............   32 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Skyline imported successfully.

Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Skyline imported successfully.

Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Skyline imported successfully.

Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Skyline cleaned successfully.

Running test_cleanRaw.R...............   33 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Skyline cleaned successfully.

Running test_cleanRaw.R...............   33 tests OK 
Running test_cleanRaw.R...............   34 tests OK 
Running test_cleanRaw.R...............   35 tests OK 
Running test_cleanRaw.R...............   36 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Skyline cleaned successfully.

Running test_cleanRaw.R...............   37 tests OK 
Running test_cleanRaw.R...............   37 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from SpectroMine imported successfully.

Running test_cleanRaw.R...............   37 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from SpectroMine imported successfully.

Running test_cleanRaw.R...............   37 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from SpectroMine cleaned successfully.

Running test_cleanRaw.R...............   37 tests OK 
Running test_cleanRaw.R...............   38 tests OK 
Running test_cleanRaw.R...............   39 tests OK ERROR [2021-05-06 04:53:51] There is no channel intensity column in the input data, which should start with 'PSM' and end with 'Raw'.

Running test_cleanRaw.R...............   40 tests OK 
Running test_cleanRaw.R...............   40 tests OK 
Running test_cleanRaw.R...............   40 tests OK 
Running test_cleanRaw.R...............   40 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Spectronaut imported successfully.

Running test_cleanRaw.R...............   40 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Spectronaut imported successfully.

Running test_cleanRaw.R...............   40 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Spectronaut cleaned successfully.

Running test_cleanRaw.R...............   40 tests OK INFO  [2021-05-06 04:53:51] ** Raw data from Spectronaut cleaned successfully.

Running test_cleanRaw.R...............   40 tests OK 
Running test_cleanRaw.R...............   41 tests OK 
Running test_cleanRaw.R...............   42 tests OK 
Running test_cleanRaw.R...............   43 tests OK 1.5s

Running test_dt.R.....................    0 tests    
Running test_dt.R.....................    0 tests    
Running test_dt.R.....................    1 tests OK 
Running test_dt.R.....................    2 tests OK 
Running test_dt.R.....................    3 tests OK 
Running test_dt.R.....................    4 tests OK 
Running test_dt.R.....................    5 tests OK 
Running test_dt.R.....................    6 tests OK 
Running test_dt.R.....................    6 tests OK 
Running test_dt.R.....................    7 tests OK 
Running test_dt.R.....................    7 tests OK 
Running test_dt.R.....................    7 tests OK 
Running test_dt.R.....................    8 tests OK 
Running test_dt.R.....................    9 tests OK 
Running test_dt.R.....................   10 tests OK 16ms

Running test_feature_cleaning.R.......    0 tests    
Running test_feature_cleaning.R.......    0 tests    
Running test_feature_cleaning.R.......    0 tests    
Running test_feature_cleaning.R.......    0 tests    INFO  [2021-05-06 04:53:51] ** Features with one or two measurements across channels within each run are removed.

Running test_feature_cleaning.R.......    1 tests OK INFO  [2021-05-06 04:53:51] ** Features with one or two measurements across runs are removed.

Running test_feature_cleaning.R.......    2 tests OK INFO  [2021-05-06 04:53:51] ** Features with one or two measurements across runs are removed.

Running test_feature_cleaning.R.......    3 tests OK 
Running test_feature_cleaning.R.......    3 tests OK 
Running test_feature_cleaning.R.......    3 tests OK INFO  [2021-05-06 04:53:51] ** Features with all missing measurements across runs are removed.

Running test_feature_cleaning.R.......    4 tests OK INFO  [2021-05-06 04:53:51] ** Features with one or two measurements across runs are removed.

Running test_feature_cleaning.R.......    5 tests OK 
Running test_feature_cleaning.R.......    5 tests OK 
Running test_feature_cleaning.R.......    5 tests OK 
Running test_feature_cleaning.R.......    6 tests OK 
Running test_feature_cleaning.R.......    6 tests OK 
Running test_feature_cleaning.R.......    6 tests OK 
Running test_feature_cleaning.R.......    6 tests OK 
Running test_feature_cleaning.R.......    7 tests OK INFO  [2021-05-06 04:53:51] ** Three isotopic preaks per feature and run are summed

Running test_feature_cleaning.R.......    8 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......    9 tests OK 
Running test_feature_cleaning.R.......   10 tests OK 
Running test_feature_cleaning.R.......   10 tests OK 
Running test_feature_cleaning.R.......   10 tests OK 
Running test_feature_cleaning.R.......   11 tests OK 
Running test_feature_cleaning.R.......   11 tests OK 
Running test_feature_cleaning.R.......   11 tests OK 
Running test_feature_cleaning.R.......   12 tests OK 
Running test_feature_cleaning.R.......   12 tests OK 
Running test_feature_cleaning.R.......   13 tests OK 
Running test_feature_cleaning.R.......   13 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   14 tests OK 
Running test_feature_cleaning.R.......   15 tests OK 
Running test_feature_cleaning.R.......   15 tests OK INFO  [2021-05-06 04:53:51] ** PSMs have been aggregated to peptide ions.

Running test_feature_cleaning.R.......   16 tests OK INFO  [2021-05-06 04:53:52] ** PSMs have been aggregated to peptide ions.

Running test_feature_cleaning.R.......   16 tests OK 
Running test_feature_cleaning.R.......   17 tests OK 
Running test_feature_cleaning.R.......   17 tests OK 
Running test_feature_cleaning.R.......   17 tests OK 
Running test_feature_cleaning.R.......   18 tests OK INFO  [2021-05-06 04:53:52] Proteins with a single feature are removed.

Running test_feature_cleaning.R.......   19 tests OK 
Running test_feature_cleaning.R.......   20 tests OK INFO  [2021-05-06 04:53:52] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2021-05-06 04:53:52] ** Features with one or two measurements across runs are removed.

Running test_feature_cleaning.R.......   20 tests OK INFO  [2021-05-06 04:53:52] ** Features with one or two measurements across channels within each run are removed.
INFO  [2021-05-06 04:53:52] ** PSMs have been aggregated to peptide ions.

Running test_feature_cleaning.R.......   20 tests OK 
Running test_feature_cleaning.R.......   21 tests OK 
Running test_feature_cleaning.R.......   22 tests OK 0.5s

Running test_filtering.R..............    0 tests    
Running test_filtering.R..............    0 tests    
Running test_filtering.R..............    1 tests OK INFO  [2021-05-06 04:53:52] ** Sequences containing \+ are removed.

Running test_filtering.R..............    2 tests OK INFO  [2021-05-06 04:53:52] ** Sequences containing \+ are removed.

Running test_filtering.R..............    3 tests OK 
Running test_filtering.R..............    4 tests OK 
Running test_filtering.R..............    5 tests OK 
Running test_filtering.R..............    6 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_1 equal to - are removed 

Running test_filtering.R..............    7 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_1 equal to +, - are removed 

Running test_filtering.R..............    8 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_1 equal to + are removed 

Running test_filtering.R..............    9 tests OK 
Running test_filtering.R..............   10 tests OK 
Running test_filtering.R..............   11 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_1 equal to R are removed 

Running test_filtering.R..............   12 tests OK 
Running test_filtering.R..............   13 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_2 equal to + are removed 

Running test_filtering.R..............   14 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_2 equal to X are removed 

Running test_filtering.R..............   15 tests OK 
Running test_filtering.R..............   16 tests OK 
Running test_filtering.R..............   17 tests OK 
Running test_filtering.R..............   18 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values greater than 0.3 in Score are removed 

Running test_filtering.R..............   19 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values greater than 0.3 in Score are removed 

Running test_filtering.R..............   20 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values greater than 0.3 in Score are removed 

Running test_filtering.R..............   21 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values greater than 0.3 in Score are removed 

Running test_filtering.R..............   22 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values smaller than 0.3 in Score are removed 

Running test_filtering.R..............   23 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values smaller than 0.3 in Score are removed 

Running test_filtering.R..............   24 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values smaller than 0.3 in Score are removed 

Running test_filtering.R..............   25 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values smaller than 0.3 in Score are removed 

Running test_filtering.R..............   26 tests OK INFO  [2021-05-06 04:53:52] ** Intensities with values greater than 0.3 in Score are replaced with NA

Running test_filtering.R..............   26 tests OK 
Running test_filtering.R..............   27 tests OK 
Running test_filtering.R..............   28 tests OK INFO  [2021-05-06 04:53:52] ** Intensities with values greater than 0.3 in Score are replaced with NA

Running test_filtering.R..............   28 tests OK 
Running test_filtering.R..............   29 tests OK 
Running test_filtering.R..............   30 tests OK INFO  [2021-05-06 04:53:52] ** Intensities with values smaller than 0.3 in Score are replaced with NA

Running test_filtering.R..............   30 tests OK 
Running test_filtering.R..............   31 tests OK 
Running test_filtering.R..............   32 tests OK INFO  [2021-05-06 04:53:52] ** Intensities with values smaller than 0.3 in Score are replaced with NA

Running test_filtering.R..............   32 tests OK 
Running test_filtering.R..............   33 tests OK 
Running test_filtering.R..............   34 tests OK 
Running test_filtering.R..............   35 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-05-06 04:53:52] ** Sequences containing \+ are removed.

Running test_filtering.R..............   36 tests OK INFO  [2021-05-06 04:53:52] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-05-06 04:53:52] ** Sequences containing \+ are removed.

Running test_filtering.R..............   37 tests OK 62ms

Running test_fractions.R..............    0 tests    
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    1 tests OK 
Running test_fractions.R..............    2 tests OK 
Running test_fractions.R..............    3 tests OK 
Running test_fractions.R..............    4 tests OK 
Running test_fractions.R..............    4 tests OK 
Running test_fractions.R..............    5 tests OK 
Running test_fractions.R..............    5 tests OK 
Running test_fractions.R..............    5 tests OK 
Running test_fractions.R..............    5 tests OK 
Running test_fractions.R..............    6 tests OK 
Running test_fractions.R..............    7 tests OK 
Running test_fractions.R..............    8 tests OK 
Running test_fractions.R..............    8 tests OK INFO  [2021-05-06 04:53:52] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2021-05-06 04:53:52] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2021-05-06 04:53:52] ** For peptides overlapped between fractions of 2_1 use the fraction with maximal average abundance.

Running test_fractions.R..............    8 tests OK 
Running test_fractions.R..............    9 tests OK 0.1s

Running test_logging.R................    1 tests OK 
Running test_logging.R................    2 tests OK 
Running test_logging.R................    3 tests OK 16ms

Running test_shared_peptides.R........    0 tests    
Running test_shared_peptides.R........    0 tests    INFO  [2021-05-06 04:53:52] ** Shared peptides are removed.

Running test_shared_peptides.R........    0 tests    
Running test_shared_peptides.R........    0 tests    INFO  [2021-05-06 04:53:52] ** Shared peptides are removed.

Running test_shared_peptides.R........    0 tests    
Running test_shared_peptides.R........    1 tests OK 
Running test_shared_peptides.R........    2 tests OK 
Running test_shared_peptides.R........    3 tests OK 
Running test_shared_peptides.R........    4 tests OK 
Running test_shared_peptides.R........    5 tests OK 16ms

Running test_workflow.R...............    0 tests    
Running test_workflow.R...............    0 tests    INFO  [2021-05-06 04:53:52] ** Raw data from OpenMS imported successfully.

Running test_workflow.R...............    0 tests    
Running test_workflow.R...............    1 tests OK INFO  [2021-05-06 04:53:52] ** Raw data from OpenMS cleaned successfully.

Running test_workflow.R...............    1 tests OK 
Running test_workflow.R...............    2 tests OK INFO  [2021-05-06 04:53:52] ** Using annotation extracted from quantification data.
INFO  [2021-05-06 04:53:52] ** Run labels were standardized to remove symbols such as '.' or '%'.

Running test_workflow.R...............    2 tests OK 
Running test_workflow.R...............    3 tests OK INFO  [2021-05-06 04:53:52] ** 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  [2021-05-06 04:53:52] ** Features with all missing measurements across runs are removed.
INFO  [2021-05-06 04:53:52] ** Shared peptides are removed.
INFO  [2021-05-06 04:53:52] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2021-05-06 04:53:52] ** Features with one or two measurements across runs are removed.
INFO  [2021-05-06 04:53:52] Proteins with a single feature are removed.
INFO  [2021-05-06 04:53:52] ** Run annotation merged with quantification data.

Running test_workflow.R...............    3 tests OK 
Running test_workflow.R...............    4 tests OK 
Running test_workflow.R...............    5 tests OK 
Running test_workflow.R...............    6 tests OK INFO  [2021-05-06 04:53:52] ** Features with one or two measurements across runs are removed.
INFO  [2021-05-06 04:53:52] ** Fractionation handled.
INFO  [2021-05-06 04:53:52] ** Updated quantification data to make balanced design. Missing values are marked by NA

Running test_workflow.R...............    6 tests OK 
Running test_workflow.R...............    7 tests OK 
Running test_workflow.R...............    8 tests OK 0.1s
All ok, 165 results (2.8s)
There were 29 warnings (use warnings() to see them)
> 
> 
> proc.time()
   user  system elapsed 
   3.28    0.20    3.48

Example timings

MSstatsConvert.Rcheck/examples_i386/MSstatsConvert-Ex.timings

nameusersystemelapsed
MSstatsBalancedDesign0.030.010.05
MSstatsClean0.270.000.31
MSstatsImport0.330.000.33
MSstatsLogsSettings0.010.000.01
MSstatsMakeAnnotation0.290.000.28
MSstatsPreprocess0.260.000.27
MSstatsSaveSessionInfo0.000.020.02
getDataType0.20.00.2
getInputFile0.270.000.26

MSstatsConvert.Rcheck/examples_x64/MSstatsConvert-Ex.timings

nameusersystemelapsed
MSstatsBalancedDesign0.050.000.05
MSstatsClean0.170.020.19
MSstatsImport0.270.000.27
MSstatsLogsSettings0.020.000.01
MSstatsMakeAnnotation0.230.000.24
MSstatsPreprocess0.190.000.18
MSstatsSaveSessionInfo0.020.000.02
getDataType0.140.000.14
getInputFile0.170.010.19