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This page was generated on 2025-10-13 11:39 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1379/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 4.16.1  (landing page)
Meena Choi
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/MSstats
git_branch: RELEASE_3_21
git_last_commit: a221510
git_last_commit_date: 2025-07-02 08:08:11 -0400 (Wed, 02 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for MSstats on merida1

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: 4.16.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstats_4.16.1.tar.gz
StartedAt: 2025-10-10 07:10:03 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 07:14:52 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 289.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MSstats.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstats_4.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MSstats.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.16.1’
* 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 ‘MSstats’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 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 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
.logMissingness: no visible binding for global variable
  ‘is_na_abundance’
.logMissingness: no visible global function definition for ‘.’
.logMissingness: no visible binding for global variable ‘LABEL’
.logMissingness: no visible binding for global variable ‘GROUP’
.logSummaryStatistics: no visible global function definition for ‘.’
.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 global function definition for ‘.’
.setCensoredByThreshold: no visible binding for global variable
  ‘PROTEIN’
.setCensoredByThreshold: no visible binding for global variable
  ‘FEATURE’
.setCensoredByThreshold: no visible binding for global variable ‘LABEL’
.setCensoredByThreshold: no visible binding for global variable
  ‘abundance_cutoff’
.setCensoredByThreshold: no visible binding for global variable
  ‘min_abundance’
.setCensoredByThreshold: no visible binding for global variable
  ‘any_censored’
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 FEATURE GROUP LABEL PROTEIN
  RUN abundance_cutoff any_censored col2rgb is_na_abundance
  min_abundance 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     17.762  0.124  18.531
dot-makeQCPlot       16.230  0.078  16.640
groupComparisonPlots  8.451  0.068   8.601
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MSstats.Rcheck/00check.log’
for details.


Installation output

MSstats.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘MSstats’ ...
** this is package ‘MSstats’ version ‘4.16.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
        #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
                ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c common.cpp -o common.o
In file included from common.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
        #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
                ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c comparison_contrasts.cpp -o comparison_contrasts.o
In file included from comparison_contrasts.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
        #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
                ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c linear_summary.cpp -o linear_summary.o
In file included from linear_summary.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
        #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
                ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c median_polish.cpp -o median_polish.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 0.1s
INFO  [2025-10-10 07:14:05] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-10 07:14:05] ** Fractionation handled.
INFO  [2025-10-10 07:14:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-10 07:14:05] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2025-10-10 07:14:05] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2025-10-10 07:14:05] ** Use all features that the dataset originally has.
INFO  [2025-10-10 07:14:05] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2025-10-10 07:14:05] 
                    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  [2025-10-10 07:14:06]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-10-10 07:14:06]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2025-10-10 07:14:06] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-10 07:14:06] ** Fractionation handled.
INFO  [2025-10-10 07:14:06] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-10 07:14:06] ** Use all features that the dataset originally has.
INFO  [2025-10-10 07:14:06] 
 # proteins: 6
 # peptides per protein: 11-32
 # features per peptide: 1-1
INFO  [2025-10-10 07:14:06] 
                    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  [2025-10-10 07:14:06] Some features are completely missing in at least one condition:  
 -.PHSHPALTPEQK_35_35_NA_NA,
 A.DIAGHGQEVLIR_321_321_NA_NA,
 A.PGFTYTDANKNK_367_367_NA_NA,
 A.PGFTYTDANK_129_129_NA_NA,
 A.PGFTYTDANK_130_130_NA_NA ...
INFO  [2025-10-10 07:14:06]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |============                                                          |  17%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-10-10 07:14:06]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2025-10-10 07:14:06] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-10 07:14:06] ** Fractionation handled.
INFO  [2025-10-10 07:14:06] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-10 07:14:06] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2025-10-10 07:14:06] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2025-10-10 07:14:06] ** Use all features that the dataset originally has.
INFO  [2025-10-10 07:14:06] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2025-10-10 07:14:06] 
                    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  [2025-10-10 07:14:06]  == Start the summarization per subplot...
INFO  [2025-10-10 07:14:14]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2025-10-10 07:14:14] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-10 07:14:14] ** Fractionation handled.
INFO  [2025-10-10 07:14:14] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-10 07:14:14] ** Use all features that the dataset originally has.
INFO  [2025-10-10 07:14:14] 
 # proteins: 6
 # peptides per protein: 11-32
 # features per peptide: 1-1
INFO  [2025-10-10 07:14:14] 
                    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  [2025-10-10 07:14:14] Some features are completely missing in at least one condition:  
 -.PHSHPALTPEQK_35_35_NA_NA,
 A.DIAGHGQEVLIR_321_321_NA_NA,
 A.PGFTYTDANKNK_367_367_NA_NA,
 A.PGFTYTDANK_129_129_NA_NA,
 A.PGFTYTDANK_130_130_NA_NA ...
INFO  [2025-10-10 07:14:14]  == Start the summarization per subplot...
INFO  [2025-10-10 07:14:22]  == Summarization is done.

test_dataProcess.R............    0 tests    
test_dataProcess.R............    1 tests OK 
test_dataProcess.R............    2 tests OK 
test_dataProcess.R............    2 tests OK INFO  [2025-10-10 07:14:22] ** Multiple fractionations exist: 4 fractionations per MS replicate.
INFO  [2025-10-10 07:14:22] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-10 07:14:22] ** Fractionation handled.
INFO  [2025-10-10 07:14:22] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-10 07:14:23] ** Log2 intensities under cutoff = 19.966  were considered as censored missing values.
INFO  [2025-10-10 07:14:23] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2025-10-10 07:14:23] ** Use all features that the dataset originally has.
INFO  [2025-10-10 07:14:23] 
 # proteins: 2
 # peptides per protein: 2-3
 # features per peptide: 1-1
INFO  [2025-10-10 07:14:23] 
                    Group1 Group2
             # runs     48     30
    # bioreplicates      7      5
 # tech. replicates      2      2
INFO  [2025-10-10 07:14:23] The following runs have more than 75% missing values: 16,
 19,
 20,
 24,
 30,
 41,
 42,
 58,
 61,
 62,
 65,
 66,
 73,
 74
INFO  [2025-10-10 07:14:23]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-10-10 07:14:23]  == Summarization is done.

test_dataProcess.R............    2 tests OK 
test_dataProcess.R............    3 tests OK 
test_dataProcess.R............    4 tests OK 17.5s
INFO  [2025-10-10 07:14:23] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-10 07:14:23] ** Fractionation handled.
INFO  [2025-10-10 07:14:23] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-10 07:14:23] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2025-10-10 07:14:23] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2025-10-10 07:14:23] ** Use all features that the dataset originally has.
INFO  [2025-10-10 07:14:23] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2025-10-10 07:14:23] 
                    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  [2025-10-10 07:14:23]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-10-10 07:14:23]  == 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  [2025-10-10 07:14:23]  == Start to test and get inference in whole plot ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-10-10 07:14:23]  == Comparisons for all proteins are done.

test_groupComparison.R........    0 tests    INFO  [2025-10-10 07:14:23]  == Start to test and get inference in whole plot ...
INFO  [2025-10-10 07:14:32]  == Comparisons for all proteins are done.

test_groupComparison.R........    0 tests    
test_groupComparison.R........    1 tests OK 9.0s

test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    INFO  [2025-10-10 07:14:32] ** Features with one or two measurements across runs are removed.
INFO  [2025-10-10 07:14:32] ** Fractionation handled.
INFO  [2025-10-10 07:14:32] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-10-10 07:14:32] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2025-10-10 07:14:32] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2025-10-10 07:14:32] ** Use all features that the dataset originally has.
INFO  [2025-10-10 07:14:32] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2025-10-10 07:14:32] 
                    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  [2025-10-10 07:14:32]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-10-10 07:14:32]  == Summarization is done.

test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    INFO  [2025-10-10 07:14:32]  == Start to test and get inference in whole plot ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-10-10 07:14:32]  == Comparisons for all proteins are done.

test_groupComparisonQCPlots.R.    0 tests    Test passed 🥳

test_groupComparisonQCPlots.R.    8 tests OK 1.7s
3ms

test_utils_censored.R.........    0 tests    
test_utils_censored.R.........    0 tests    
test_utils_censored.R.........    0 tests    
test_utils_censored.R.........    0 tests    
test_utils_censored.R.........    1 tests OK 
test_utils_censored.R.........    1 tests OK 
test_utils_censored.R.........    2 tests OK 
test_utils_censored.R.........    2 tests OK 
test_utils_censored.R.........    3 tests OK 
test_utils_censored.R.........    3 tests OK 
test_utils_censored.R.........    3 tests OK 
test_utils_censored.R.........    3 tests OK 
test_utils_censored.R.........    3 tests OK 
test_utils_censored.R.........    4 tests OK 67ms

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 33ms

test_utils_statistics.R.......    0 tests    
test_utils_statistics.R.......    0 tests    
test_utils_statistics.R.......    0 tests    
test_utils_statistics.R.......    0 tests    
test_utils_statistics.R.......    0 tests    
test_utils_statistics.R.......    0 tests    
test_utils_statistics.R.......    0 tests    
test_utils_statistics.R.......    1 tests OK 
test_utils_statistics.R.......    2 tests OK 
test_utils_statistics.R.......    3 tests OK 
test_utils_statistics.R.......    4 tests OK 
test_utils_statistics.R.......    5 tests OK 
test_utils_statistics.R.......    5 tests OK 
test_utils_statistics.R.......    5 tests OK 
test_utils_statistics.R.......    5 tests OK 
test_utils_statistics.R.......    5 tests OK 
test_utils_statistics.R.......    5 tests OK 
test_utils_statistics.R.......    5 tests OK 
test_utils_statistics.R.......    5 tests OK 
test_utils_statistics.R.......    6 tests OK 
test_utils_statistics.R.......    7 tests OK 59ms
All ok, 30 results (28.4s)
> 
> proc.time()
   user  system elapsed 
 11.220   0.734  35.956 

Example timings

MSstats.Rcheck/MSstats-Ex.timings

nameusersystemelapsed
DDARawData0.0080.0030.013
DDARawData.Skyline0.0080.0030.011
DIARawData0.0060.0020.007
MSstatsGroupComparison0.9200.0711.048
MSstatsGroupComparisonOutput0.6290.0860.742
MSstatsGroupComparisonSingleProtein0.4070.0060.430
MSstatsHandleMissing0.1190.0090.133
MSstatsMergeFractions0.1230.0070.138
MSstatsNormalize0.1060.0040.116
MSstatsPrepareForDataProcess0.0990.0050.109
MSstatsPrepareForGroupComparison0.3170.0080.337
MSstatsPrepareForSummarization0.1100.0060.121
MSstatsSelectFeatures0.4450.0220.483
MSstatsSummarizationOutput0.5480.0140.592
MSstatsSummarizeSingleLinear0.1560.0060.171
MSstatsSummarizeSingleTMP0.2070.0060.220
MSstatsSummarizeWithSingleCore0.5090.0090.544
SDRFtoAnnotation0.0510.0090.063
SRMRawData0.0050.0020.009
checkRepeatedDesign0.3120.0040.328
dataProcess0.9680.0241.005
dataProcessPlots17.762 0.12418.531
designSampleSize0.5950.0230.662
designSampleSizePlots0.6330.0200.807
dot-makeQCPlot16.230 0.07816.640
example_SDRF0.0180.0080.026
extractSDRF0.3020.0170.321
getProcessed0.1230.0090.133
getSamplesInfo0.5970.0090.618
groupComparison0.5000.0100.516
groupComparisonPlots8.4510.0688.601
groupComparisonQCPlots2.3980.0202.426
makePeptidesDictionary0.0070.0010.008
modelBasedQCPlots2.4360.0222.480
quantification0.3940.0110.409