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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1350/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 4.14.0  (landing page)
Meena Choi
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MSstats
git_branch: RELEASE_3_20
git_last_commit: 3585528
git_last_commit_date: 2024-10-29 09:48:46 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for MSstats on nebbiolo2

To the developers/maintainers of the MSstats package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstats.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MSstats
Version: 4.14.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MSstats_4.14.0.tar.gz
StartedAt: 2024-12-20 03:16:21 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 03:21:59 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 337.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MSstats.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MSstats_4.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MSstats.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstats’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘MSstatsConvert:::.standardizeColnames’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotHeatmap : <anonymous>: no visible global function definition for
  ‘col2rgb’
.plotProfile: no visible binding for global variable ‘newABUNDANCE’
.savePlotlyPlotHTML: no visible global function definition for ‘zip’
.setCensoredByThreshold: no visible binding for global variable
  ‘any_censored’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘DetectionQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalQValue’
MSstatsPrepareForSummarization: no visible binding for global variable
  ‘ref’
MSstatsPrepareForSummarization: no visible binding for global variable
  ‘LABEL’
MSstatsPrepareForSummarization: no visible binding for global variable
  ‘RUN’
SDRFtoAnnotation: no visible binding for global variable
  ‘..extract_cols’
extractSDRF: no visible binding for global variable ‘..extract_cols’
validateAnnotation: no visible binding for global variable
  ‘BioReplicate’
validateAnnotation: no visible binding for global variable ‘Condition’
Undefined global functions or variables:
  ..extract_cols BioReplicate Condition DetectionQValue GlobalPGQValue
  GlobalQValue LABEL LibPGQValue LibQValue RUN any_censored col2rgb
  newABUNDANCE ref zip
Consider adding
  importFrom("grDevices", "col2rgb")
  importFrom("utils", "zip")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) MSstatsSummarizationOutput.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MSstatsSummarizationOutput.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MSstatsSummarizationOutput.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
* 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 ... WARNING
Documented arguments not in \usage in Rd file 'dot-documentFunction.Rd':
  ‘removeFewMeasurements’ ‘useUniquePeptide’ ‘summaryforMultipleRows’
  ‘removeProtein_with1Feature’ ‘removeProtein_with1Peptide’
  ‘removeOxidationMpeptides’ ‘removeMpeptides’ ‘use_log_file’ ‘append’
  ‘verbose’ ‘log_file_path’

Documented arguments not in \usage in Rd file 'dot-getContrast.Rd':
  ‘contrast_matrix’

Documented arguments not in \usage in Rd file 'dot-getSingleProteinForProfile.Rd':
  ‘dataProcess’

Documented arguments not in \usage in Rd file 'dot-getWideTable.Rd':
  ‘vector’

Undocumented arguments in Rd file 'modelBasedQCPlots.Rd'
  ‘displayDeprecationMessage’

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
dataProcessPlots 5.253  0.093   5.218
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MSstats.Rcheck/00check.log’
for details.


Installation output

MSstats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MSstats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘MSstats’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c common.cpp -o common.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c comparison_contrasts.cpp -o comparison_contrasts.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c linear_summary.cpp -o linear_summary.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c median_polish.cpp -o median_polish.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-MSstats/00new/MSstats/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstats)

Tests output

MSstats.Rcheck/tests/tinytest.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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) ){
+   tinytest::test_package("MSstats")
+ }

Attaching package: 'MSstats'

The following object is masked from 'package:grDevices':

    savePlot


test_MSstatsdev.R.............    1 tests OK 48ms
INFO  [2024-12-20 03:21:29] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:21:29] ** Fractionation handled.
INFO  [2024-12-20 03:21:29] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:21:29] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-12-20 03:21:29] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-12-20 03:21:29] ** Use all features that the dataset originally has.
INFO  [2024-12-20 03:21:29] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-12-20 03:21:29] 
                    1 2 3 4 5 6 7 8 9 10
             # runs 3 3 3 3 3 3 3 3 3  3
    # bioreplicates 3 3 3 3 3 3 3 3 3  3
 # tech. replicates 1 1 1 1 1 1 1 1 1  1
INFO  [2024-12-20 03:21:29]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-12-20 03:21:29]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2024-12-20 03:21:29] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:21:29] ** Fractionation handled.
INFO  [2024-12-20 03:21:29] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:21:29] ** Use all features that the dataset originally has.
INFO  [2024-12-20 03:21:29] 
 # proteins: 6
 # peptides per protein: 11-32
 # features per peptide: 1-1
INFO  [2024-12-20 03:21:29] 
                    C1 C2 C3 C4 C5 C6
             # runs  3  3  3  3  3  3
    # bioreplicates  1  1  1  1  1  1
 # tech. replicates  3  3  3  3  3  3
INFO  [2024-12-20 03:21:29] Some features are completely missing in at least one condition:  
 D.GPLTGTYR_23_23_NA_NA,
 F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA,
 G.PLTGTYR_8_8_NA_NA,
 H.SFNVEYDDSQDK_465_465_NA_NA,
 K.AVVQDPALKPL_156_156_NA_NA ...
INFO  [2024-12-20 03:21:29]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |============                                                          |  17%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-12-20 03:21:29]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2024-12-20 03:21:29] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:21:29] ** Fractionation handled.
INFO  [2024-12-20 03:21:29] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:21:29] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-12-20 03:21:29] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-12-20 03:21:29] ** Use all features that the dataset originally has.
INFO  [2024-12-20 03:21:29] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-12-20 03:21:29] 
                    1 2 3 4 5 6 7 8 9 10
             # runs 3 3 3 3 3 3 3 3 3  3
    # bioreplicates 3 3 3 3 3 3 3 3 3  3
 # tech. replicates 1 1 1 1 1 1 1 1 1  1
INFO  [2024-12-20 03:21:29]  == Start the summarization per subplot...
INFO  [2024-12-20 03:21:32]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2024-12-20 03:21:32] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:21:32] ** Fractionation handled.
INFO  [2024-12-20 03:21:32] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:21:32] ** Use all features that the dataset originally has.
INFO  [2024-12-20 03:21:32] 
 # proteins: 6
 # peptides per protein: 11-32
 # features per peptide: 1-1
INFO  [2024-12-20 03:21:32] 
                    C1 C2 C3 C4 C5 C6
             # runs  3  3  3  3  3  3
    # bioreplicates  1  1  1  1  1  1
 # tech. replicates  3  3  3  3  3  3
INFO  [2024-12-20 03:21:32] Some features are completely missing in at least one condition:  
 D.GPLTGTYR_23_23_NA_NA,
 F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA,
 G.PLTGTYR_8_8_NA_NA,
 H.SFNVEYDDSQDK_465_465_NA_NA,
 K.AVVQDPALKPL_156_156_NA_NA ...
INFO  [2024-12-20 03:21:32]  == Start the summarization per subplot...
INFO  [2024-12-20 03:21:35]  == Summarization is done.

test_dataProcess.R............    0 tests    
test_dataProcess.R............    1 tests OK 
test_dataProcess.R............    2 tests OK 6.5s
INFO  [2024-12-20 03:21:35] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:21:35] ** Fractionation handled.
INFO  [2024-12-20 03:21:35] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:21:35] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-12-20 03:21:35] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-12-20 03:21:35] ** Use all features that the dataset originally has.
INFO  [2024-12-20 03:21:35] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-12-20 03:21:35] 
                    1 2 3 4 5 6 7 8 9 10
             # runs 3 3 3 3 3 3 3 3 3  3
    # bioreplicates 3 3 3 3 3 3 3 3 3  3
 # tech. replicates 1 1 1 1 1 1 1 1 1  1
INFO  [2024-12-20 03:21:35]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-12-20 03:21:35]  == Summarization is done.

test_groupComparison.R........    0 tests    
test_groupComparison.R........    0 tests    
test_groupComparison.R........    0 tests    
test_groupComparison.R........    0 tests    
test_groupComparison.R........    0 tests    INFO  [2024-12-20 03:21:35]  == Start to test and get inference in whole plot ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-12-20 03:21:36]  == Comparisons for all proteins are done.

test_groupComparison.R........    0 tests    INFO  [2024-12-20 03:21:36]  == Start to test and get inference in whole plot ...
INFO  [2024-12-20 03:21:39]  == Comparisons for all proteins are done.

test_groupComparison.R........    0 tests    
test_groupComparison.R........    1 tests OK 3.5s

test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    INFO  [2024-12-20 03:21:39] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:21:39] ** Fractionation handled.
INFO  [2024-12-20 03:21:39] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:21:39] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-12-20 03:21:39] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-12-20 03:21:39] ** Use all features that the dataset originally has.
INFO  [2024-12-20 03:21:39] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-12-20 03:21:39] 
                    1 2 3 4 5 6 7 8 9 10
             # runs 3 3 3 3 3 3 3 3 3  3
    # bioreplicates 3 3 3 3 3 3 3 3 3  3
 # tech. replicates 1 1 1 1 1 1 1 1 1  1
INFO  [2024-12-20 03:21:39]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-12-20 03:21:39]  == Summarization is done.

test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    INFO  [2024-12-20 03:21:39]  == Start to test and get inference in whole plot ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-12-20 03:21:39]  == Comparisons for all proteins are done.

test_groupComparisonQCPlots.R.    0 tests    Test passed 🥳

test_groupComparisonQCPlots.R.    8 tests OK 0.6s
1ms

test_utils_groupcomparison_checks.R    0 tests    
test_utils_groupcomparison_checks.R    1 tests OK 
test_utils_groupcomparison_checks.R    1 tests OK 
test_utils_groupcomparison_checks.R    2 tests OK 
test_utils_groupcomparison_checks.R    2 tests OK 
test_utils_groupcomparison_checks.R    3 tests OK 
test_utils_groupcomparison_checks.R    3 tests OK 
test_utils_groupcomparison_checks.R    4 tests OK 
test_utils_groupcomparison_checks.R    4 tests OK 
test_utils_groupcomparison_checks.R    5 tests OK 13ms
All ok, 17 results (10.6s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  4.200   0.454  13.285 

Example timings

MSstats.Rcheck/MSstats-Ex.timings

nameusersystemelapsed
DDARawData0.0040.0010.005
DDARawData.Skyline0.0040.0010.005
DIANNtoMSstatsFormat000
DIARawData0.0020.0000.002
DIAUmpiretoMSstatsFormat0.1080.0020.097
FragPipetoMSstatsFormat0.0440.0030.037
MSstatsGroupComparison0.2650.0120.256
MSstatsGroupComparisonOutput0.2300.0010.198
MSstatsGroupComparisonSingleProtein0.2180.0000.175
MSstatsHandleMissing0.0870.0000.046
MSstatsMergeFractions0.0980.0010.050
MSstatsNormalize0.0810.0000.042
MSstatsPrepareForDataProcess0.0670.0060.040
MSstatsPrepareForGroupComparison0.1350.0020.119
MSstatsPrepareForSummarization0.0710.0000.038
MSstatsSelectFeatures0.3080.0070.209
MSstatsSummarizationOutput0.2850.0000.222
MSstatsSummarize0.2620.0010.207
MSstatsSummarizeSingleLinear0.1140.0010.068
MSstatsSummarizeSingleTMP0.1290.0040.082
MSstatsSummarizeWithSingleCore0.2580.0030.211
MaxQtoMSstatsFormat0.1370.0030.085
OpenMStoMSstatsFormat0.0540.0000.043
OpenSWATHtoMSstatsFormat0.0570.0010.047
PDtoMSstatsFormat0.0550.0010.045
ProgenesistoMSstatsFormat0.0570.0010.047
SDRFtoAnnotation0.0090.0000.009
SRMRawData0.0010.0000.001
SkylinetoMSstatsFormat0.0990.0010.072
SpectronauttoMSstatsFormat0.0580.0000.043
checkRepeatedDesign0.1670.0000.133
dataProcess0.4610.0230.360
dataProcessPlots5.2530.0935.218
designSampleSize0.2540.0070.217
designSampleSizePlots0.2640.0060.226
dot-makeQCPlot4.7920.0464.727
example_SDRF0.0060.0000.007
extractSDRF0.1910.0010.126
getProcessed0.1020.0050.054
getSamplesInfo0.3490.0010.262
groupComparison0.2080.0010.191
groupComparisonPlots2.4060.0162.404
groupComparisonQCPlots0.7490.0050.714
makePeptidesDictionary0.0050.0000.003
modelBasedQCPlots0.7500.0010.695
quantification0.2050.0020.163