Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:23 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for MSstatsConvert on machv2


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? 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 1228/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsConvert 1.4.1  (landing page)
Mateusz Staniak
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MSstatsConvert
git_branch: RELEASE_3_14
git_last_commit: 4593789
git_last_commit_date: 2022-02-14 17:11:42 -0400 (Mon, 14 Feb 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MSstatsConvert
Version: 1.4.1
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_1.4.1.tar.gz
StartedAt: 2022-04-12 15:51:46 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:52:35 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 48.5 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_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MSstatsConvert.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK
* this is package ‘MSstatsConvert’ version ‘1.4.1’
* 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.findAvailable’ ‘.standardizeColnames’
* checking S3 generic/method consistency ... WARNING
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
.cleanRawPhilosopher: no visible binding for global variable
  ‘ModifiedPeptideSequence’
.cleanRawPhilosopher: no visible binding for global variable
  ‘PeptideSequence’
.cleanRawPhilosopher: no visible binding for global variable ‘IsUnique’
.cleanRawPhilosopher: no visible binding for global variable ‘PSM’
.cleanRawPhilosopher: no visible binding for global variable
  ‘PrecursorCharge’
.cleanRawPhilosopher: no visible binding for global variable
  ‘Intensity’
.cleanRawPhilosopher: no visible binding for global variable ‘Run’
.cleanRawPhilosopher: no visible binding for global variable
  ‘ProteinName’
.summarizeMultiplePSMs: no visible binding for global variable ‘Purity’
.summarizeMultiplePSMs: no visible binding for global variable
  ‘PeptideProphet.Probability’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘ModifiedPeptideSequence’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘PeptideSequence’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘IsUnique’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘PSM’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘PrecursorCharge’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘Intensity’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘Run’
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
  variable ‘ProteinName’
Undefined global functions or variables:
  Intensity IsUnique ModifiedPeptideSequence PSM
  PeptideProphet.Probability PeptideSequence PrecursorCharge
  ProteinName 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/MSstatsConvert.Rcheck/00check.log’
for details.

Installation output

MSstatsConvert.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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  [2022-04-12 15:52:24] ** Using annotation extracted from quantification data.
INFO  [2022-04-12 15:52:24] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    1 tests OK INFO  [2022-04-12 15:52:24] ** Using provided annotation.
INFO  [2022-04-12 15:52:24] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    2 tests OK 
test_annotation.R.............    2 tests OK INFO  [2022-04-12 15:52:24] ** Using provided annotation.
INFO  [2022-04-12 15:52:24] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    3 tests OK INFO  [2022-04-12 15:52:24] ** Using provided annotation.
INFO  [2022-04-12 15:52:24] ** 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  [2022-04-12 15:52:24] ** Run annotation merged with quantification data.

test_annotation.R.............    6 tests OK INFO  [2022-04-12 15:52:24] ** Using provided annotation.
INFO  [2022-04-12 15:52:24] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    6 tests OK INFO  [2022-04-12 15:52:24] ** Run annotation merged with quantification data.

test_annotation.R.............    7 tests OK INFO  [2022-04-12 15:52:24] ** Using provided annotation.
INFO  [2022-04-12 15:52:24] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_annotation.R.............    7 tests OK 
test_annotation.R.............    8 tests OK INFO  [2022-04-12 15:52:24] ** Using provided annotation.
INFO  [2022-04-12 15:52:24] ** 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  [2022-04-12 15:52:24] ** 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  [2022-04-12 15:52:24] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2022-04-12 15:52:24] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2022-04-12 15:52:24] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    
test_cleanRaw.R...............    0 tests    INFO  [2022-04-12 15:52:24] ** Raw data from DIAUmpire imported successfully.

test_cleanRaw.R...............    0 tests    INFO  [2022-04-12 15:52:24] ** Using selected fragments and peptides.
INFO  [2022-04-12 15:52:24] ** Extracted the data from selected fragments and/or peptides.
INFO  [2022-04-12 15:52:24] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2022-04-12 15:52:24] ** Using selected fragments and peptides.
INFO  [2022-04-12 15:52:24] ** Extracted the data from selected fragments and/or peptides.
INFO  [2022-04-12 15:52:24] ** Raw data from DIAUmpire cleaned successfully.

test_cleanRaw.R...............    0 tests    INFO  [2022-04-12 15:52:24] ** Using selected fragments.
INFO  [2022-04-12 15:52:24] ** Extracted the data from selected fragments and/or peptides.
INFO  [2022-04-12 15:52:24] ** 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  [2022-04-12 15:52:24] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2022-04-12 15:52:24] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-04-12 15:52:24] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2022-04-12 15:52:24] ** Raw data from MaxQuant cleaned successfully.

test_cleanRaw.R...............    9 tests OK INFO  [2022-04-12 15:52:24] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2022-04-12 15:52:24] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2022-04-12 15:52:24] ** 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  [2022-04-12 15:52:24] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-04-12 15:52:24] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2022-04-12 15:52:24] ** 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  [2022-04-12 15:52:24] ** Raw data from MaxQuant imported successfully.

test_cleanRaw.R...............   13 tests OK INFO  [2022-04-12 15:52:24] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-04-12 15:52:24] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-04-12 15:52:24] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2022-04-12 15:52:25] ** Features with all missing measurements across channels within each run are removed.
INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   15 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from OpenMS cleaned successfully.

test_cleanRaw.R...............   15 tests OK 
test_cleanRaw.R...............   16 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Raw data from OpenMS imported successfully.

test_cleanRaw.R...............   18 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Raw data from OpenSWATH imported successfully.

test_cleanRaw.R...............   20 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   22 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from ProteomeDiscoverer imported successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from ProteomeDiscoverer cleaned successfully.

test_cleanRaw.R...............   25 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from Progenesis imported successfully.

test_cleanRaw.R...............   30 tests OK 
test_cleanRaw.R...............   30 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from Progenesis cleaned successfully.

test_cleanRaw.R...............   30 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from Skyline imported successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   33 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Raw data from Skyline cleaned successfully.

test_cleanRaw.R...............   37 tests OK 
test_cleanRaw.R...............   37 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from SpectroMine imported successfully.

test_cleanRaw.R...............   37 tests OK INFO  [2022-04-12 15:52:25] ** 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 [2022-04-12 15:52:25] 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  [2022-04-12 15:52:25] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from Spectronaut imported successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2022-04-12 15:52:25] ** Raw data from Spectronaut cleaned successfully.

test_cleanRaw.R...............   40 tests OK INFO  [2022-04-12 15:52:25] ** 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 1.3s

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 23ms

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  [2022-04-12 15:52:25] ** Features with one or two measurements across channels within each run are removed.

test_feature_cleaning.R.......    1 tests OK INFO  [2022-04-12 15:52:25] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......    2 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Features with all missing measurements across runs are removed.

test_feature_cleaning.R.......    4 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** PSMs have been aggregated to peptide ions.

test_feature_cleaning.R.......   16 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] Proteins with a single feature are removed.

test_feature_cleaning.R.......   19 tests OK 
test_feature_cleaning.R.......   20 tests OK INFO  [2022-04-12 15:52:25] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2022-04-12 15:52:25] ** Features with one or two measurements across runs are removed.

test_feature_cleaning.R.......   20 tests OK INFO  [2022-04-12 15:52:25] ** Features with one or two measurements across channels within each run are removed.
INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Sequences containing \+ are removed.

test_filtering.R..............    2 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Rows with values of Symbol_1 equal to - are removed 

test_filtering.R..............    7 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values of Symbol_1 equal to +, - are removed 

test_filtering.R..............    8 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Rows with values of Symbol_1 equal to R are removed 

test_filtering.R..............   12 tests OK 
test_filtering.R..............   13 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2022-04-12 15:52:25] ** Rows with values of Symbol_2 equal to + are removed 

test_filtering.R..............   14 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values of Symbol_1 equal to X are removed 
INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   19 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   20 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   21 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values not greater than 0.3 in Score are removed 

test_filtering.R..............   22 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   23 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   24 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   25 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values not smaller than 0.3 in Score are removed 

test_filtering.R..............   26 tests OK INFO  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** 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  [2022-04-12 15:52:25] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2022-04-12 15:52:25] ** Sequences containing \+ are removed.

test_filtering.R..............   36 tests OK INFO  [2022-04-12 15:52:25] ** Rows with values of Symbol_1 equal to + are removed 
INFO  [2022-04-12 15:52:26] ** Sequences containing \+ are removed.

test_filtering.R..............   37 tests OK 65ms

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  [2022-04-12 15:52:26] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2022-04-12 15:52:26] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO  [2022-04-12 15:52:26] ** 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 4ms

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2022-04-12 15:52:26] ** Shared peptides are removed.

test_shared_peptides.R........    0 tests    
test_shared_peptides.R........    0 tests    INFO  [2022-04-12 15:52:26] ** 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 17ms

test_workflow.R...............    0 tests    
test_workflow.R...............    0 tests    INFO  [2022-04-12 15:52:26] ** Raw data from OpenMS imported successfully.

test_workflow.R...............    0 tests    
test_workflow.R...............    1 tests OK INFO  [2022-04-12 15:52:26] ** Raw data from OpenMS cleaned successfully.

test_workflow.R...............    1 tests OK 
test_workflow.R...............    2 tests OK INFO  [2022-04-12 15:52:26] ** Using annotation extracted from quantification data.
INFO  [2022-04-12 15:52:26] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_workflow.R...............    2 tests OK 
test_workflow.R...............    3 tests OK INFO  [2022-04-12 15:52:26] ** 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  [2022-04-12 15:52:26] ** Features with all missing measurements across runs are removed.
INFO  [2022-04-12 15:52:26] ** Shared peptides are removed.
INFO  [2022-04-12 15:52:26] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2022-04-12 15:52:26] ** Features with one or two measurements across runs are removed.
INFO  [2022-04-12 15:52:26] Proteins with a single feature are removed.
INFO  [2022-04-12 15:52:26] ** 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  [2022-04-12 15:52:26] ** Features with one or two measurements across runs are removed.
INFO  [2022-04-12 15:52:26] ** Fractionation handled.
INFO  [2022-04-12 15:52:26] ** 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 97ms
All ok, 165 results (2.4s)
There were 29 warnings (use warnings() to see them)
> 
> 
> proc.time()
   user  system elapsed 
  2.938   0.224   3.214

Example timings

MSstatsConvert.Rcheck/MSstatsConvert-Ex.timings

nameusersystemelapsed
MSstatsBalancedDesign0.0690.0060.076
MSstatsClean0.2340.0180.253
MSstatsImport0.2110.0110.222
MSstatsLogsSettings0.0210.0020.023
MSstatsMakeAnnotation0.3660.0060.372
MSstatsPreprocess0.2180.0130.231
MSstatsSaveSessionInfo0.0170.0080.024
getDataType0.1590.0080.167
getInputFile0.1100.0070.118