Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:13 -0400 (Fri, 15 Oct 2021).

CHECK results for MSstatsConvert on tokay2

To the developers/maintainers of the MSstatsConvert package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1209/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsConvert 1.2.2  (landing page)
Mateusz Staniak
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MSstatsConvert
git_branch: RELEASE_3_13
git_last_commit: bcc4339
git_last_commit_date: 2021-06-15 09:03:32 -0400 (Tue, 15 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSstatsConvert
Version: 1.2.2
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsConvert.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MSstatsConvert_1.2.2.tar.gz
StartedAt: 2021-10-15 02:23:05 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 02:23:58 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 52.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsConvert.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsConvert.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MSstatsConvert_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSstatsConvert.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.2.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MSstatsConvert_1.2.2.tar.gz && rm -rf MSstatsConvert.buildbin-libdir && mkdir MSstatsConvert.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstatsConvert.buildbin-libdir MSstatsConvert_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MSstatsConvert_1.2.2.zip && rm MSstatsConvert_1.2.2.tar.gz MSstatsConvert_1.2.2.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  587k  100  587k    0     0  1713k      0 --:--:-- --:--:-- --:--:-- 1711k

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_1.2.2.zip
* DONE (MSstatsConvert)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MSstatsConvert' successfully unpacked and MD5 sums checked

Tests output

MSstatsConvert.Rcheck/tests_i386/tinytest.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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")
+ }

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 0.2s

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  [2021-10-15 02:23:45] ** Using annotation extracted from quantification data.
INFO  [2021-10-15 02:23:45] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    1 tests OK INFO  [2021-10-15 02:23:45] ** Using provided annotation.
INFO  [2021-10-15 02:23:45] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    2 tests OK 
test_annotation.R.............    2 tests OK INFO  [2021-10-15 02:23:45] ** Using provided annotation.
INFO  [2021-10-15 02:23:45] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    3 tests OK INFO  [2021-10-15 02:23:45] ** Using provided annotation.
INFO  [2021-10-15 02:23:45] ** 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  [2021-10-15 02:23:45] ** Run annotation merged with quantification data.

test_annotation.R.............    6 tests OK INFO  [2021-10-15 02:23:45] ** Using provided annotation.
INFO  [2021-10-15 02:23:45] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    6 tests OK INFO  [2021-10-15 02:23:45] ** Run annotation merged with quantification data.

test_annotation.R.............    7 tests OK INFO  [2021-10-15 02:23:45] ** Using provided annotation.
INFO  [2021-10-15 02:23:45] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    7 tests OK 
test_annotation.R.............    8 tests OK INFO  [2021-10-15 02:23:45] ** Using provided annotation.
INFO  [2021-10-15 02:23:45] ** 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  [2021-10-15 02:23:45] ** Using provided annotation.

test_annotation.R.............   11 tests OK 94ms

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 0.2s

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:45] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:45] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:45] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:45] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:45] ** Using selected fragments and peptides.
INFO  [2021-10-15 02:23:45] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-10-15 02:23:45] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:45] ** Using selected fragments and peptides.
INFO  [2021-10-15 02:23:45] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-10-15 02:23:45] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:45] ** Using selected fragments.
INFO  [2021-10-15 02:23:45] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-10-15 02:23:45] ** 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  [2021-10-15 02:23:46] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2021-10-15 02:23:46] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:46] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-10-15 02:23:46] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2021-10-15 02:23:46] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2021-10-15 02:23:46] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2021-10-15 02:23:46] ** 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  [2021-10-15 02:23:46] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:46] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-10-15 02:23:46] ** 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  [2021-10-15 02:23:46] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............   13 tests OK INFO  [2021-10-15 02:23:46] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:46] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:46] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-10-15 02:23:46] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-10-15 02:23:46] ** 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  [2021-10-15 02:23:46] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   15 tests OK 
test_cleanRaw.R...............   16 tests OK INFO  [2021-10-15 02:23:46] ** 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  [2021-10-15 02:23:46] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   18 tests OK INFO  [2021-10-15 02:23:46] ** 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  [2021-10-15 02:23:46] ** Raw data from OpenSWATH imported successfully.

test_cleanRaw.R...............   20 tests OK INFO  [2021-10-15 02:23:46] ** 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  [2021-10-15 02:23:46] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2021-10-15 02:23:46] ** 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  [2021-10-15 02:23:46] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:46] ** 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  [2021-10-15 02:23:46] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK 
test_cleanRaw.R...............   30 tests OK INFO  [2021-10-15 02:23:46] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2021-10-15 02:23:46] ** 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  [2021-10-15 02:23:47] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2021-10-15 02:23:47] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2021-10-15 02:23:47] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2021-10-15 02:23:47] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2021-10-15 02:23:47] ** 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  [2021-10-15 02:23:47] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   37 tests OK 
test_cleanRaw.R...............   37 tests OK INFO  [2021-10-15 02:23:47] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2021-10-15 02:23:47] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2021-10-15 02:23:47] ** 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 [2021-10-15 02:23:47] 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  [2021-10-15 02:23:47] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2021-10-15 02:23:47] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2021-10-15 02:23:47] ** Raw data from Spectronaut cleaned successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2021-10-15 02:23:47] ** 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 1.9s

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.....................    6 tests OK 
test_dt.R.....................    7 tests OK 
test_dt.R.....................    7 tests OK 
test_dt.R.....................    7 tests OK 
test_dt.R.....................    8 tests OK 
test_dt.R.....................    9 tests OK 
test_dt.R.....................   10 tests OK 16ms

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  [2021-10-15 02:23:47] ** Features with one or two measurements across channels within each run are removed.

test_feature_cleaning.R.......    1 tests OK INFO  [2021-10-15 02:23:47] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    2 tests OK INFO  [2021-10-15 02:23:47] ** 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  [2021-10-15 02:23:47] ** Features with all missing measurements across runs are removed.

test_feature_cleaning.R.......    4 tests OK INFO  [2021-10-15 02:23:47] ** 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  [2021-10-15 02:23:47] ** 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  [2021-10-15 02:23:47] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests OK INFO  [2021-10-15 02:23:47] ** 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  [2021-10-15 02:23:47] Proteins with a single feature are removed.

test_feature_cleaning.R.......   19 tests OK 
test_feature_cleaning.R.......   20 tests OK INFO  [2021-10-15 02:23:47] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2021-10-15 02:23:47] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......   20 tests OK INFO  [2021-10-15 02:23:47] ** Features with one or two measurements across channels within each run are removed.
INFO  [2021-10-15 02:23:47] ** 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 0.5s

test_filtering.R..............    0 tests    
test_filtering.R..............    0 tests    
test_filtering.R..............    1 tests OK INFO  [2021-10-15 02:23:47] ** Sequences containing \+ are removed.

test_filtering.R..............    2 tests OK INFO  [2021-10-15 02:23:47] ** 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  [2021-10-15 02:23:47] ** Rows with values of Symbol_1 equal to - are removed 

test_filtering.R..............    7 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values of Symbol_1 equal to +, - are removed 

test_filtering.R..............    8 tests OK INFO  [2021-10-15 02:23:47] ** 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  [2021-10-15 02:23:47] ** Rows with values of Symbol_1 equal to R are removed 

test_filtering.R..............   12 tests OK 
test_filtering.R..............   13 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-10-15 02:23:47] ** Rows with values of Symbol_2 equal to + are removed 

test_filtering.R..............   14 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2021-10-15 02:23:47] ** 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  [2021-10-15 02:23:47] ** Rows with values greater than 0.3 in Score are removed 

test_filtering.R..............   19 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values greater than 0.3 in Score are removed 

test_filtering.R..............   20 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values greater than 0.3 in Score are removed 

test_filtering.R..............   21 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values greater than 0.3 in Score are removed 

test_filtering.R..............   22 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values smaller than 0.3 in Score are removed 

test_filtering.R..............   23 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values smaller than 0.3 in Score are removed 

test_filtering.R..............   24 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values smaller than 0.3 in Score are removed 

test_filtering.R..............   25 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values smaller than 0.3 in Score are removed 

test_filtering.R..............   26 tests OK INFO  [2021-10-15 02:23:47] ** Intensities with values 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  [2021-10-15 02:23:47] ** Intensities with values 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  [2021-10-15 02:23:47] ** Intensities with values 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  [2021-10-15 02:23:47] ** Intensities with values 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  [2021-10-15 02:23:47] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-10-15 02:23:47] ** Sequences containing \+ are removed.

test_filtering.R..............   36 tests OK INFO  [2021-10-15 02:23:47] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-10-15 02:23:47] ** Sequences containing \+ are removed.

test_filtering.R..............   37 tests OK 78ms

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  [2021-10-15 02:23:48] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2021-10-15 02:23:48] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2021-10-15 02:23:48] ** 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 0.1s

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

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2021-10-15 02:23:48] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2021-10-15 02:23:48] ** 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 16ms

test_workflow.R...............    0 tests    
test_workflow.R...............    0 tests    INFO  [2021-10-15 02:23:48] ** Raw data from OpenMS imported successfully.

test_workflow.R...............    0 tests    
test_workflow.R...............    1 tests OK INFO  [2021-10-15 02:23:48] ** Raw data from OpenMS cleaned successfully.

test_workflow.R...............    1 tests OK 
test_workflow.R...............    2 tests OK INFO  [2021-10-15 02:23:48] ** Using annotation extracted from quantification data.
INFO  [2021-10-15 02:23:48] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_workflow.R...............    2 tests OK 
test_workflow.R...............    3 tests OK INFO  [2021-10-15 02:23:48] ** 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  [2021-10-15 02:23:48] ** Features with all missing measurements across runs are removed.
INFO  [2021-10-15 02:23:48] ** Shared peptides are removed.
INFO  [2021-10-15 02:23:48] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2021-10-15 02:23:48] ** Features with one or two measurements across runs are removed.
INFO  [2021-10-15 02:23:48] Proteins with a single feature are removed.
INFO  [2021-10-15 02:23:48] ** 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  [2021-10-15 02:23:48] ** Features with one or two measurements across runs are removed.
INFO  [2021-10-15 02:23:48] ** Fractionation handled.
INFO  [2021-10-15 02:23:48] ** 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 78ms
All ok, 165 results (3.2s)
There were 29 warnings (use warnings() to see them)
> 
> 
> proc.time()
   user  system elapsed 
   2.96    0.17    3.95

MSstatsConvert.Rcheck/tests_x64/tinytest.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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")
+ }

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 0.2s

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  [2021-10-15 02:23:49] ** Using annotation extracted from quantification data.
INFO  [2021-10-15 02:23:49] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    1 tests OK INFO  [2021-10-15 02:23:49] ** Using provided annotation.
INFO  [2021-10-15 02:23:49] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    2 tests OK 
test_annotation.R.............    2 tests OK INFO  [2021-10-15 02:23:49] ** Using provided annotation.
INFO  [2021-10-15 02:23:49] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    3 tests OK INFO  [2021-10-15 02:23:49] ** Using provided annotation.
INFO  [2021-10-15 02:23:49] ** 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  [2021-10-15 02:23:49] ** Run annotation merged with quantification data.

test_annotation.R.............    6 tests OK INFO  [2021-10-15 02:23:49] ** Using provided annotation.
INFO  [2021-10-15 02:23:49] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    6 tests OK INFO  [2021-10-15 02:23:49] ** Run annotation merged with quantification data.

test_annotation.R.............    7 tests OK INFO  [2021-10-15 02:23:49] ** Using provided annotation.
INFO  [2021-10-15 02:23:49] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    7 tests OK 
test_annotation.R.............    8 tests OK INFO  [2021-10-15 02:23:49] ** Using provided annotation.
INFO  [2021-10-15 02:23:49] ** 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  [2021-10-15 02:23:49] ** 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 0.2s

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:49] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:49] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:49] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:49] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:49] ** Using selected fragments and peptides.
INFO  [2021-10-15 02:23:49] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-10-15 02:23:49] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:49] ** Using selected fragments and peptides.
INFO  [2021-10-15 02:23:49] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-10-15 02:23:49] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2021-10-15 02:23:49] ** Using selected fragments.
INFO  [2021-10-15 02:23:49] ** Extracted the data from selected fragments and/or peptides.
INFO  [2021-10-15 02:23:49] ** 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  [2021-10-15 02:23:50] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:50] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-10-15 02:23:50] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2021-10-15 02:23:50] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:50] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............   13 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:23:50] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-10-15 02:23:50] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   15 tests OK 
test_cleanRaw.R...............   16 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   18 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Raw data from OpenSWATH imported successfully.

test_cleanRaw.R...............   20 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK 
test_cleanRaw.R...............   30 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   37 tests OK 
test_cleanRaw.R...............   37 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2021-10-15 02:23:50] ** 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 [2021-10-15 02:23:50] 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  [2021-10-15 02:23:50] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2021-10-15 02:23:50] ** Raw data from Spectronaut cleaned successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2021-10-15 02:23:50] ** 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 1.0s

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.....................    6 tests OK 
test_dt.R.....................    7 tests OK 
test_dt.R.....................    7 tests OK 
test_dt.R.....................    7 tests OK 
test_dt.R.....................    8 tests OK 
test_dt.R.....................    9 tests OK 
test_dt.R.....................   10 tests OK 16ms

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  [2021-10-15 02:23:50] ** Features with one or two measurements across channels within each run are removed.

test_feature_cleaning.R.......    1 tests OK INFO  [2021-10-15 02:23:50] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    2 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Features with all missing measurements across runs are removed.

test_feature_cleaning.R.......    4 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] Proteins with a single feature are removed.

test_feature_cleaning.R.......   19 tests OK 
test_feature_cleaning.R.......   20 tests OK INFO  [2021-10-15 02:23:50] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2021-10-15 02:23:50] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......   20 tests OK INFO  [2021-10-15 02:23:50] ** Features with one or two measurements across channels within each run are removed.
INFO  [2021-10-15 02:23:50] ** PSMs have been aggregated to peptide ions.

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

test_filtering.R..............    0 tests    
test_filtering.R..............    0 tests    
test_filtering.R..............    1 tests OK INFO  [2021-10-15 02:23:50] ** Sequences containing \+ are removed.

test_filtering.R..............    2 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Rows with values of Symbol_1 equal to - are removed 

test_filtering.R..............    7 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values of Symbol_1 equal to +, - are removed 

test_filtering.R..............    8 tests OK INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Rows with values of Symbol_1 equal to R are removed 

test_filtering.R..............   12 tests OK 
test_filtering.R..............   13 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Rows with values of Symbol_2 equal to + are removed 

test_filtering.R..............   14 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2021-10-15 02:23:50] ** 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  [2021-10-15 02:23:50] ** Rows with values greater than 0.3 in Score are removed 

test_filtering.R..............   19 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values greater than 0.3 in Score are removed 

test_filtering.R..............   20 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values greater than 0.3 in Score are removed 

test_filtering.R..............   21 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values greater than 0.3 in Score are removed 

test_filtering.R..............   22 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values smaller than 0.3 in Score are removed 

test_filtering.R..............   23 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values smaller than 0.3 in Score are removed 

test_filtering.R..............   24 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values smaller than 0.3 in Score are removed 

test_filtering.R..............   25 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values smaller than 0.3 in Score are removed 

test_filtering.R..............   26 tests OK INFO  [2021-10-15 02:23:50] ** Intensities with values 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  [2021-10-15 02:23:50] ** Intensities with values 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  [2021-10-15 02:23:50] ** Intensities with values 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  [2021-10-15 02:23:50] ** Intensities with values 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  [2021-10-15 02:23:50] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Sequences containing \+ are removed.

test_filtering.R..............   36 tests OK INFO  [2021-10-15 02:23:50] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2021-10-15 02:23:50] ** Sequences containing \+ are removed.

test_filtering.R..............   37 tests OK 47ms

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  [2021-10-15 02:23:51] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2021-10-15 02:23:51] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2021-10-15 02:23:51] ** 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 78ms

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

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2021-10-15 02:23:51] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2021-10-15 02:23:51] ** 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 16ms

test_workflow.R...............    0 tests    
test_workflow.R...............    0 tests    INFO  [2021-10-15 02:23:51] ** Raw data from OpenMS imported successfully.

test_workflow.R...............    0 tests    
test_workflow.R...............    1 tests OK INFO  [2021-10-15 02:23:51] ** Raw data from OpenMS cleaned successfully.

test_workflow.R...............    1 tests OK 
test_workflow.R...............    2 tests OK INFO  [2021-10-15 02:23:51] ** Using annotation extracted from quantification data.
INFO  [2021-10-15 02:23:51] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_workflow.R...............    2 tests OK 
test_workflow.R...............    3 tests OK INFO  [2021-10-15 02:23:51] ** 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  [2021-10-15 02:23:51] ** Features with all missing measurements across runs are removed.
INFO  [2021-10-15 02:23:51] ** Shared peptides are removed.
INFO  [2021-10-15 02:23:51] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2021-10-15 02:23:51] ** Features with one or two measurements across runs are removed.
INFO  [2021-10-15 02:23:51] Proteins with a single feature are removed.
INFO  [2021-10-15 02:23:51] ** 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  [2021-10-15 02:23:51] ** Features with one or two measurements across runs are removed.
INFO  [2021-10-15 02:23:51] ** Fractionation handled.
INFO  [2021-10-15 02:23:51] ** 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 78ms
All ok, 165 results (2.0s)
There were 29 warnings (use warnings() to see them)
> 
> 
> proc.time()
   user  system elapsed 
   2.48    0.09    2.57

Example timings

MSstatsConvert.Rcheck/examples_i386/MSstatsConvert-Ex.timings

nameusersystemelapsed
MSstatsBalancedDesign0.080.010.13
MSstatsClean0.500.020.62
MSstatsImport0.480.020.50
MSstatsLogsSettings0.000.010.02
MSstatsMakeAnnotation0.410.000.42
MSstatsPreprocess0.400.000.42
MSstatsSaveSessionInfo0.030.000.03
getDataType0.250.000.25
getInputFile0.240.000.23

MSstatsConvert.Rcheck/examples_x64/MSstatsConvert-Ex.timings

nameusersystemelapsed
MSstatsBalancedDesign0.080.000.14
MSstatsClean0.310.030.34
MSstatsImport0.310.000.32
MSstatsLogsSettings0.020.000.01
MSstatsMakeAnnotation0.280.000.28
MSstatsPreprocess0.200.050.24
MSstatsSaveSessionInfo0.000.010.01
getDataType0.180.030.21
getInputFile0.170.000.17