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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1315/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsConvert 1.10.5  (landing page)
Mateusz Staniak
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MSstatsConvert
git_branch: RELEASE_3_17
git_last_commit: 8261c57
git_last_commit_date: 2023-07-28 09:14:01 -0400 (Fri, 28 Jul 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for MSstatsConvert on kjohnson2


To the developers/maintainers of the MSstatsConvert package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: MSstatsConvert
Version: 1.10.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsConvert_1.10.5.tar.gz
StartedAt: 2023-10-18 10:02:49 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 10:03:58 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 68.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MSstatsConvert.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsConvert_1.10.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSstatsConvert.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK
* this is package ‘MSstatsConvert’ version ‘1.10.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsConvert’ can be installed ... OK
* 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
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
as.data.table:
  function(x, keep.rownames, ...)
as.data.table.MSstatsValidated:
  function(x)

as.data.frame:
  function(x, row.names, optional, ...)
as.data.frame.MSstatsValidated:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.cleanRawDIANN: no visible binding for global variable ‘PrecursorMz’
.cleanRawDIANN: no visible binding for global variable ‘FragmentInfo’
.cleanRawDIANN: no visible binding for global variable
  ‘FragmentQuantCorrected’
.cleanRawDIANN: no visible binding for global variable ‘FragmentIon’
.cleanRawDIANN: no visible binding for global variable ‘ProductCharge’
.cleanRawDIANN: no visible binding for global variable
  ‘PeptideSequence’
.cleanRawPhilosopher: no visible binding for global variable ‘Run’
.summarizeMultiplePSMs: no visible binding for global variable ‘Purity’
.summarizeMultiplePSMs: no visible binding for global variable
  ‘PeptideProphet.Probability’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘PrecursorMz’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘FragmentInfo’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘FragmentQuantCorrected’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘FragmentIon’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘ProductCharge’
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
  ‘PeptideSequence’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘Run’
Undefined global functions or variables:
  FragmentInfo FragmentIon FragmentQuantCorrected
  PeptideProphet.Probability PeptideSequence PrecursorMz ProductCharge
  Purity Run
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'getInputFile' and siglist 'MSstatsPhilosopherFiles'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'MSstatsClean'
  ‘channels’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes 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: 3 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSstatsConvert.Rcheck/00check.log’
for details.

Installation output

MSstatsConvert.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘MSstatsConvert’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsConvert)

Tests output

MSstatsConvert.Rcheck/tests/tinytest.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 0.1s

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  [2023-10-18 10:03:38] ** Using annotation extracted from quantification data.
INFO  [2023-10-18 10:03:38] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    1 tests OK INFO  [2023-10-18 10:03:38] ** Using provided annotation.
INFO  [2023-10-18 10:03:38] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    2 tests OK 
test_annotation.R.............    2 tests OK INFO  [2023-10-18 10:03:38] ** Using provided annotation.
INFO  [2023-10-18 10:03:38] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    3 tests OK INFO  [2023-10-18 10:03:38] ** Using provided annotation.
INFO  [2023-10-18 10:03:38] ** 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  [2023-10-18 10:03:38] ** Run annotation merged with quantification data.

test_annotation.R.............    6 tests OK INFO  [2023-10-18 10:03:38] ** Using provided annotation.
INFO  [2023-10-18 10:03:38] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    6 tests OK INFO  [2023-10-18 10:03:38] ** Run annotation merged with quantification data.

test_annotation.R.............    7 tests OK INFO  [2023-10-18 10:03:38] ** Using provided annotation.
INFO  [2023-10-18 10:03:38] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    7 tests OK 
test_annotation.R.............    8 tests OK INFO  [2023-10-18 10:03:38] ** Using provided annotation.
INFO  [2023-10-18 10:03:38] ** 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  [2023-10-18 10:03:38] ** 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  [2023-10-18 10:03:38] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2023-10-18 10:03:38] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2023-10-18 10:03:38] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2023-10-18 10:03:38] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2023-10-18 10:03:38] ** Using selected fragments and peptides.
INFO  [2023-10-18 10:03:38] ** Extracted the data from selected fragments and/or peptides.
INFO  [2023-10-18 10:03:38] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2023-10-18 10:03:38] ** Using selected fragments and peptides.
INFO  [2023-10-18 10:03:38] ** Extracted the data from selected fragments and/or peptides.
INFO  [2023-10-18 10:03:38] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2023-10-18 10:03:38] ** Using selected fragments.
INFO  [2023-10-18 10:03:38] ** Extracted the data from selected fragments and/or peptides.
INFO  [2023-10-18 10:03:38] ** 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  [2023-10-18 10:03:39] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2023-10-18 10:03:39] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-18 10:03:39] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2023-10-18 10:03:39] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2023-10-18 10:03:39] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2023-10-18 10:03:39] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-18 10:03:39] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............   13 tests OK INFO  [2023-10-18 10:03:39] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-18 10:03:39] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-18 10:03:39] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2023-10-18 10:03:39] ** Features with all missing measurements across channels within each run are removed.
INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   15 tests OK 
test_cleanRaw.R...............   16 tests OK INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   18 tests OK INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Raw data from OpenSWATH imported successfully.

test_cleanRaw.R...............   20 tests OK INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK 
test_cleanRaw.R...............   30 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   37 tests OK 
test_cleanRaw.R...............   37 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2023-10-18 10:03:39] ** 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 [2023-10-18 10:03:39] 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  [2023-10-18 10:03:39] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2023-10-18 10:03:39] ** Raw data from Spectronaut cleaned successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2023-10-18 10:03:39] ** 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 1.2s

test_dt.R.....................    0 tests    
test_dt.R.....................    0 tests    
test_dt.R.....................    1 tests OK 
test_dt.R.....................    2 tests OK 
test_dt.R.....................    3 tests OK 
test_dt.R.....................    4 tests OK 
test_dt.R.....................    5 tests OK 
test_dt.R.....................    6 tests OK 
test_dt.R.....................    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  [2023-10-18 10:03:39] ** Features with one or two measurements across channels within each run are removed.

test_feature_cleaning.R.......    1 tests OK INFO  [2023-10-18 10:03:39] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    2 tests OK INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** Features with all missing measurements across runs are removed.

test_feature_cleaning.R.......    4 tests OK INFO  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:39] ** 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  [2023-10-18 10:03:40] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests OK INFO  [2023-10-18 10:03:40] ** 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  [2023-10-18 10:03:40] Proteins with a single feature are removed.

test_feature_cleaning.R.......   19 tests OK 
test_feature_cleaning.R.......   20 tests OK INFO  [2023-10-18 10:03:40] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2023-10-18 10:03:40] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......   20 tests OK INFO  [2023-10-18 10:03:40] ** Features with one or two measurements across channels within each run are removed.
INFO  [2023-10-18 10:03:40] ** 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  [2023-10-18 10:03:40] ** Sequences containing \+ are removed.

test_filtering.R..............    2 tests OK INFO  [2023-10-18 10:03:40] ** 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  [2023-10-18 10:03:40] ** Rows with values of Symbol_1 equal to - are removed 

test_filtering.R..............    7 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values of Symbol_1 equal to +, - are removed 

test_filtering.R..............    8 tests OK INFO  [2023-10-18 10:03:40] ** 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  [2023-10-18 10:03:40] ** Rows with values of Symbol_1 equal to R are removed 

test_filtering.R..............   12 tests OK 
test_filtering.R..............   13 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2023-10-18 10:03:40] ** Rows with values of Symbol_2 equal to + are removed 

test_filtering.R..............   14 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2023-10-18 10:03:40] ** 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  [2023-10-18 10:03:40] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   19 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   20 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   21 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   22 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   23 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   24 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   25 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   26 tests OK INFO  [2023-10-18 10:03:40] ** Intensities with values not greater than 0.3 in Score are replaced with NA

test_filtering.R..............   26 tests OK 
test_filtering.R..............   27 tests OK 
test_filtering.R..............   28 tests OK INFO  [2023-10-18 10:03:40] ** Intensities with values not greater than 0.3 in Score are replaced with NA

test_filtering.R..............   28 tests OK 
test_filtering.R..............   29 tests OK 
test_filtering.R..............   30 tests OK INFO  [2023-10-18 10:03:40] ** Intensities with values not smaller than 0.3 in Score are replaced with NA

test_filtering.R..............   30 tests OK 
test_filtering.R..............   31 tests OK 
test_filtering.R..............   32 tests OK INFO  [2023-10-18 10:03:40] ** Intensities with values not smaller than 0.3 in Score are replaced with NA

test_filtering.R..............   32 tests OK 
test_filtering.R..............   33 tests OK 
test_filtering.R..............   34 tests OK 
test_filtering.R..............   35 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2023-10-18 10:03:40] ** Sequences containing \+ are removed.

test_filtering.R..............   36 tests OK INFO  [2023-10-18 10:03:40] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2023-10-18 10:03:40] ** Sequences containing \+ are removed.

test_filtering.R..............   37 tests OK 63ms

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  [2023-10-18 10:03:40] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2023-10-18 10:03:40] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2023-10-18 10:03:40] ** 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 6ms

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2023-10-18 10:03:40] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2023-10-18 10:03:40] ** 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 23ms

test_workflow.R...............    0 tests    
test_workflow.R...............    0 tests    INFO  [2023-10-18 10:03:40] ** Raw data from OpenMS imported successfully.

test_workflow.R...............    0 tests    
test_workflow.R...............    1 tests OK INFO  [2023-10-18 10:03:40] ** Raw data from OpenMS cleaned successfully.

test_workflow.R...............    1 tests OK 
test_workflow.R...............    2 tests OK INFO  [2023-10-18 10:03:40] ** Using annotation extracted from quantification data.
INFO  [2023-10-18 10:03:40] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_workflow.R...............    2 tests OK 
test_workflow.R...............    3 tests OK INFO  [2023-10-18 10:03:40] ** 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  [2023-10-18 10:03:40] ** Features with all missing measurements across runs are removed.
INFO  [2023-10-18 10:03:40] ** Shared peptides are removed.
INFO  [2023-10-18 10:03:40] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2023-10-18 10:03:40] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:03:40] Proteins with a single feature are removed.
INFO  [2023-10-18 10:03:40] ** 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  [2023-10-18 10:03:40] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:03:40] ** Fractionation handled.
INFO  [2023-10-18 10:03:40] ** 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 0.1s
All ok, 165 results (2.5s)
There were 29 warnings (use warnings() to see them)
> 
> 
> proc.time()
   user  system elapsed 
  1.966   0.193   3.379

Example timings

MSstatsConvert.Rcheck/MSstatsConvert-Ex.timings

nameusersystemelapsed
MSstatsBalancedDesign0.0440.0050.077
MSstatsClean0.2050.0170.342
MSstatsImport0.1790.0070.283
MSstatsLogsSettings0.0130.0010.022
MSstatsMakeAnnotation0.2110.0060.329
MSstatsPreprocess0.2200.0070.352
MSstatsSaveSessionInfo0.0100.0060.020
getDataType0.1150.0050.171
getInputFile0.1230.0090.196