Meena Choi
| Snapshot Date: 2026-01-22 13:40 -0500 (Thu, 22 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/MSstats |
| git_branch: devel |
| git_last_commit: c7d33c0 |
| git_last_commit_date: 2026-01-22 12:57:41 -0500 (Thu, 22 Jan 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-23 11:34 -0500 (Fri, 23 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4808 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4542 |
| 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 1390/2345 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstats 4.19.1 (landing page) Meena Choi
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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. |
| Package: MSstats |
| Version: 4.19.1 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSstats_4.19.1.tar.gz |
| StartedAt: 2026-01-23 01:51:05 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 01:53:45 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 160.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSstats.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSstats_4.19.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MSstats.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.19.1’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
Obsolete C++11 standard request will be ignored
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
.calculate_weights: no visible binding for global variable ‘w_stats’
.calculate_weights: no visible global function definition for ‘pca’
.countMissingPercentage: no visible binding for global variable ‘GROUP’
.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 ‘.’
.normalize_anomalies: no visible binding for global variable
‘local_min’
.normalize_anomalies: no visible binding for global variable
‘ANOMALYSCORES’
.normalize_anomalies: no visible binding for global variable ‘PEPTIDE’
.normalize_anomalies: no visible binding for global variable
‘normalized_score’
.plotHeatmap : <anonymous>: no visible global function definition for
‘col2rgb’
.plotProfile: no visible binding for global variable ‘Variance’
.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’
.updateColumnsForProcessing: no visible binding for global variable
‘ANOMALYSCORES’
MSstatsPrepareForSummarization: no visible binding for global variable
‘ANOMALYSCORES’
MSstatsPrepareForSummarization: no visible binding for global variable
‘ref’
MSstatsPrepareForSummarization: no visible binding for global variable
‘LABEL’
MSstatsPrepareForSummarization: no visible binding for global variable
‘RUN’
MSstatsSummarizeSingleLinear: no visible binding for global variable
‘n_obs’
MSstatsSummarizeSingleLinear: no visible binding for global variable
‘n_obs_run’
MSstatsSummarizeSingleLinear: no visible binding for global variable
‘LABEL’
MSstatsSummarizeSingleLinear: no visible binding for global variable
‘predicted’
MSstatsSummarizeSingleLinear: no visible binding for global variable
‘censored’
MSstatsSummarizeSingleLinear: no visible binding for global variable
‘newABUNDANCE’
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 ANOMALYSCORES BioReplicate Condition FEATURE GROUP
LABEL PEPTIDE PROTEIN RUN Variance abundance_cutoff any_censored
censored col2rgb is_na_abundance local_min min_abundance n_obs
n_obs_run newABUNDANCE normalized_score pca predicted ref w_stats zip
Consider adding
importFrom("grDevices", "col2rgb")
importFrom("utils", "zip")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 ... INFO
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 7.871 0.213 7.968
dot-makeQCPlot 6.884 0.137 6.880
* 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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/MSstats.Rcheck/00check.log’
for details.
MSstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MSstats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘MSstats’ ... ** this is package ‘MSstats’ version ‘4.19.1’ ** using staged installation ** libs specified C++11 using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c common.cpp -o common.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c comparison_contrasts.cpp -o comparison_contrasts.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c linear_summary.cpp -o linear_summary.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c median_polish.cpp -o median_polish.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-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-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-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)
MSstats.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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 [0;32mOK[0m [0;36m47ms[0m
INFO [2026-01-23 01:52:57] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:52:57] ** Fractionation handled.
INFO [2026-01-23 01:52:57] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:52:57] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values.
INFO [2026-01-23 01:52:57] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:52:57] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:52:57]
# proteins: 2
# peptides per protein: 2-2
# features per peptide: 3-3
INFO [2026-01-23 01:52:57]
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 [2026-01-23 01:52:57] == Start the summarization per subplot...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:52:57] == Summarization is done.
test_dataProcess.R............ 0 tests INFO [2026-01-23 01:52:57] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:52:57] ** Fractionation handled.
INFO [2026-01-23 01:52:57] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:52:57] ** Log2 intensities under cutoff = 13.456 were considered as censored missing values.
INFO [2026-01-23 01:52:57] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:52:57] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:52:57]
# proteins: 6
# peptides per protein: 11-32
# features per peptide: 1-1
INFO [2026-01-23 01:52:57]
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 [2026-01-23 01:52:57] 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 [2026-01-23 01:52:57] == Start the summarization per subplot...
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
INFO [2026-01-23 01:52:58] == Summarization is done.
test_dataProcess.R............ 0 tests INFO [2026-01-23 01:52:58] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:52:58] ** Fractionation handled.
INFO [2026-01-23 01:52:58] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:52:58] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values.
INFO [2026-01-23 01:52:58] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:52:58] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:52:58]
# proteins: 2
# peptides per protein: 2-2
# features per peptide: 3-3
INFO [2026-01-23 01:52:58]
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 [2026-01-23 01:52:58] == Start the summarization per subplot...
INFO [2026-01-23 01:53:02] == Summarization is done.
test_dataProcess.R............ 0 tests INFO [2026-01-23 01:53:02] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:53:02] ** Fractionation handled.
INFO [2026-01-23 01:53:02] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:53:02] ** Log2 intensities under cutoff = 13.456 were considered as censored missing values.
INFO [2026-01-23 01:53:02] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:53:02] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:53:02]
# proteins: 6
# peptides per protein: 11-32
# features per peptide: 1-1
INFO [2026-01-23 01:53:02]
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 [2026-01-23 01:53:02] 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 [2026-01-23 01:53:02] == Start the summarization per subplot...
INFO [2026-01-23 01:53:06] == Summarization is done.
test_dataProcess.R............ 0 tests
test_dataProcess.R............ 1 tests [0;32mOK[0m
test_dataProcess.R............ 2 tests [0;32mOK[0m
test_dataProcess.R............ 2 tests [0;32mOK[0m INFO [2026-01-23 01:53:06] ** Multiple fractionations exist: 4 fractionations per MS replicate.
INFO [2026-01-23 01:53:06] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:53:06] ** Fractionation handled.
INFO [2026-01-23 01:53:06] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:53:06] ** Log2 intensities under cutoff = 19.966 were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:53:06]
# proteins: 2
# peptides per protein: 2-3
# features per peptide: 1-1
INFO [2026-01-23 01:53:06]
Group1 Group2
# runs 48 30
# bioreplicates 7 5
# tech. replicates 2 2
INFO [2026-01-23 01:53:06] The following runs have more than 75% missing values: 16,
19,
20,
24,
30,
41,
42,
58,
61,
62,
65,
66,
73,
74
INFO [2026-01-23 01:53:06] == Start the summarization per subplot...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:06] == Summarization is done.
test_dataProcess.R............ 2 tests [0;32mOK[0m
test_dataProcess.R............ 3 tests [0;32mOK[0m
test_dataProcess.R............ 4 tests [0;32mOK[0m
test_dataProcess.R............ 4 tests [0;32mOK[0m
test_dataProcess.R............ 5 tests [0;32mOK[0m INFO [2026-01-23 01:53:06] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:53:06] ** Fractionation handled.
INFO [2026-01-23 01:53:06] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:53:06] ** Log2 intensities under cutoff = 9.5425 were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:53:06]
# proteins: 2
# peptides per protein: 2-3
# features per peptide: 1-1
INFO [2026-01-23 01:53:06]
A B
# runs 3 2
# bioreplicates 3 2
# tech. replicates 1 1
INFO [2026-01-23 01:53:06] == Start the summarization per subplot...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:06] == Summarization is done.
test_dataProcess.R............ 5 tests [0;32mOK[0m
test_dataProcess.R............ 6 tests [0;32mOK[0m
test_dataProcess.R............ 6 tests [0;32mOK[0m
test_dataProcess.R............ 7 tests [0;32mOK[0m
test_dataProcess.R............ 8 tests [0;32mOK[0m
test_dataProcess.R............ 8 tests [0;32mOK[0m
test_dataProcess.R............ 9 tests [0;32mOK[0m
test_dataProcess.R............ 9 tests [0;32mOK[0m INFO [2026-01-23 01:53:06] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:53:06] ** Fractionation handled.
INFO [2026-01-23 01:53:06] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:53:06] ** Log2 intensities under cutoff = 9.5425 were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:53:06]
# proteins: 2
# peptides per protein: 2-3
# features per peptide: 1-1
INFO [2026-01-23 01:53:06]
A B
# runs 3 2
# bioreplicates 3 2
# tech. replicates 1 1
INFO [2026-01-23 01:53:06] == Start the summarization per subplot...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:06] == Summarization is done.
test_dataProcess.R............ 9 tests [0;32mOK[0m
test_dataProcess.R............ 9 tests [0;32mOK[0m
test_dataProcess.R............ 9 tests [0;32mOK[0m
test_dataProcess.R............ 10 tests [0;32mOK[0m
test_dataProcess.R............ 10 tests [0;32mOK[0m INFO [2026-01-23 01:53:06] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:53:06] ** Fractionation handled.
INFO [2026-01-23 01:53:06] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:53:06] ** Log2 intensities under cutoff = 9.5425 were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:53:06]
# proteins: 2
# peptides per protein: 2-3
# features per peptide: 1-1
INFO [2026-01-23 01:53:06]
A B
# runs 3 2
# bioreplicates 3 2
# tech. replicates 1 1
INFO [2026-01-23 01:53:06] == Start the summarization per subplot...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:06] == Summarization is done.
test_dataProcess.R............ 10 tests [0;32mOK[0m
test_dataProcess.R............ 10 tests [0;32mOK[0m
test_dataProcess.R............ 11 tests [0;32mOK[0m
test_dataProcess.R............ 11 tests [0;32mOK[0m
test_dataProcess.R............ 11 tests [0;32mOK[0m
test_dataProcess.R............ 11 tests [0;32mOK[0m
test_dataProcess.R............ 11 tests [0;32mOK[0m
test_dataProcess.R............ 12 tests [0;32mOK[0m
test_dataProcess.R............ 13 tests [0;32mOK[0m
test_dataProcess.R............ 14 tests [0;32mOK[0m
test_dataProcess.R............ 15 tests [0;32mOK[0m
test_dataProcess.R............ 16 tests [0;32mOK[0m
test_dataProcess.R............ 17 tests [0;32mOK[0m
test_dataProcess.R............ 18 tests [0;32mOK[0m
test_dataProcess.R............ 19 tests [0;32mOK[0m
test_dataProcess.R............ 19 tests [0;32mOK[0m
test_dataProcess.R............ 19 tests [0;32mOK[0m
test_dataProcess.R............ 25 tests [0;32mOK[0m
test_dataProcess.R............ 25 tests [0;32mOK[0m
test_dataProcess.R............ 25 tests [0;32mOK[0m
test_dataProcess.R............ 26 tests [0;32mOK[0m
test_dataProcess.R............ 26 tests [0;32mOK[0m
test_dataProcess.R............ 26 tests [0;32mOK[0m
test_dataProcess.R............ 26 tests [0;32mOK[0m
test_dataProcess.R............ 28 tests [0;32mOK[0m [0;34m9.2s[0m
INFO [2026-01-23 01:53:06] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:53:06] ** Fractionation handled.
INFO [2026-01-23 01:53:06] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:53:06] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:53:06] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:53:06]
# proteins: 2
# peptides per protein: 2-2
# features per peptide: 3-3
INFO [2026-01-23 01:53:06]
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 [2026-01-23 01:53:06] == Start the summarization per subplot...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:06] == 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 [2026-01-23 01:53:06] == Start to test and get inference in whole plot ...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:07] == Comparisons for all proteins are done.
test_groupComparison.R........ 0 tests INFO [2026-01-23 01:53:07] == Start to test and get inference in whole plot ...
INFO [2026-01-23 01:53:10] == Comparisons for all proteins are done.
test_groupComparison.R........ 0 tests
test_groupComparison.R........ 1 tests [0;32mOK[0m
test_groupComparison.R........ 1 tests [0;32mOK[0m
test_groupComparison.R........ 1 tests [0;32mOK[0m
test_groupComparison.R........ 1 tests [0;32mOK[0m
test_groupComparison.R........ 1 tests [0;32mOK[0m
test_groupComparison.R........ 1 tests [0;32mOK[0m INFO [2026-01-23 01:53:10] == Start to test and get inference in whole plot ...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:11] == Comparisons for all proteins are done.
test_groupComparison.R........ 1 tests [0;32mOK[0m INFO [2026-01-23 01:53:11] == Start to test and get inference in whole plot ...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:11] == Comparisons for all proteins are done.
test_groupComparison.R........ 1 tests [0;32mOK[0m
test_groupComparison.R........ 1 tests [0;32mOK[0m
test_groupComparison.R........ 1 tests [0;32mOK[0m
test_groupComparison.R........ 2 tests [0;32mOK[0m
test_groupComparison.R........ 3 tests [0;32mOK[0m
test_groupComparison.R........ 4 tests [0;32mOK[0m
test_groupComparison.R........ 5 tests [0;32mOK[0m
test_groupComparison.R........ 5 tests [0;32mOK[0m
test_groupComparison.R........ 5 tests [0;32mOK[0m
test_groupComparison.R........ 6 tests [0;32mOK[0m
test_groupComparison.R........ 7 tests [0;32mOK[0m
test_groupComparison.R........ 8 tests [0;32mOK[0m
test_groupComparison.R........ 9 tests [0;32mOK[0m [0;34m4.3s[0m
test_groupComparisonQCPlots.R. 0 tests
test_groupComparisonQCPlots.R. 0 tests
test_groupComparisonQCPlots.R. 0 tests INFO [2026-01-23 01:53:11] ** Features with one or two measurements across runs are removed.
INFO [2026-01-23 01:53:11] ** Fractionation handled.
INFO [2026-01-23 01:53:11] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2026-01-23 01:53:11] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values.
INFO [2026-01-23 01:53:11] ** Log2 intensities = NA were considered as censored missing values.
INFO [2026-01-23 01:53:11] ** Use top100 features that have highest average of log2(intensity) across runs.
INFO [2026-01-23 01:53:11]
# proteins: 2
# peptides per protein: 2-2
# features per peptide: 3-3
INFO [2026-01-23 01:53:11]
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 [2026-01-23 01:53:11] == Start the summarization per subplot...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:11] == Summarization is done.
test_groupComparisonQCPlots.R. 0 tests
test_groupComparisonQCPlots.R. 0 tests
test_groupComparisonQCPlots.R. 0 tests
test_groupComparisonQCPlots.R. 0 tests INFO [2026-01-23 01:53:11] == Start to test and get inference in whole plot ...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
INFO [2026-01-23 01:53:11] == Comparisons for all proteins are done.
test_groupComparisonQCPlots.R. 0 tests Test passed with 1 success 🥳.
test_groupComparisonQCPlots.R. 8 tests [0;32mOK[0m [0;34m0.7s[0m
[0;36m1ms[0m
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 [0;32mOK[0m
test_utils_censored.R......... 1 tests [0;32mOK[0m
test_utils_censored.R......... 2 tests [0;32mOK[0m
test_utils_censored.R......... 2 tests [0;32mOK[0m
test_utils_censored.R......... 3 tests [0;32mOK[0m
test_utils_censored.R......... 3 tests [0;32mOK[0m
test_utils_censored.R......... 3 tests [0;32mOK[0m
test_utils_censored.R......... 3 tests [0;32mOK[0m
test_utils_censored.R......... 3 tests [0;32mOK[0m
test_utils_censored.R......... 4 tests [0;32mOK[0m [0;36m35ms[0m
test_utils_groupComparison_model.R 0 tests
test_utils_groupComparison_model.R 0 tests
test_utils_groupComparison_model.R 1 tests [0;32mOK[0m
test_utils_groupComparison_model.R 1 tests [0;32mOK[0m
test_utils_groupComparison_model.R 2 tests [0;32mOK[0m [0;36m4ms[0m
test_utils_groupcomparison.R.. 0 tests
test_utils_groupcomparison.R.. 0 tests
test_utils_groupcomparison.R.. 0 tests
test_utils_groupcomparison.R.. 0 tests
test_utils_groupcomparison.R.. 0 tests
test_utils_groupcomparison.R.. 0 tests
test_utils_groupcomparison.R.. 1 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 2 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 3 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 4 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 5 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 5 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 5 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 5 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 5 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 5 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 5 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 5 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 5 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 6 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 7 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 7 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 7 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 7 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 7 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 7 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 7 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 8 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 9 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 10 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 11 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 12 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 13 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 14 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 15 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 16 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 17 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 17 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 17 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 17 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 17 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 17 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 17 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 17 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 18 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 19 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 20 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 21 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 22 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 23 tests [0;32mOK[0m
test_utils_groupcomparison.R.. 24 tests [0;32mOK[0m [0;36m29ms[0m
test_utils_groupcomparison_checks.R 0 tests
test_utils_groupcomparison_checks.R 1 tests [0;32mOK[0m
test_utils_groupcomparison_checks.R 1 tests [0;32mOK[0m
test_utils_groupcomparison_checks.R 2 tests [0;32mOK[0m
test_utils_groupcomparison_checks.R 2 tests [0;32mOK[0m
test_utils_groupcomparison_checks.R 3 tests [0;32mOK[0m
test_utils_groupcomparison_checks.R 3 tests [0;32mOK[0m
test_utils_groupcomparison_checks.R 4 tests [0;32mOK[0m
test_utils_groupcomparison_checks.R 4 tests [0;32mOK[0m
test_utils_groupcomparison_checks.R 5 tests [0;32mOK[0m [0;36m16ms[0m
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 [0;32mOK[0m
test_utils_statistics.R....... 2 tests [0;32mOK[0m
test_utils_statistics.R....... 3 tests [0;32mOK[0m
test_utils_statistics.R....... 4 tests [0;32mOK[0m
test_utils_statistics.R....... 5 tests [0;32mOK[0m
test_utils_statistics.R....... 5 tests [0;32mOK[0m
test_utils_statistics.R....... 5 tests [0;32mOK[0m
test_utils_statistics.R....... 5 tests [0;32mOK[0m
test_utils_statistics.R....... 5 tests [0;32mOK[0m
test_utils_statistics.R....... 5 tests [0;32mOK[0m
test_utils_statistics.R....... 5 tests [0;32mOK[0m
test_utils_statistics.R....... 5 tests [0;32mOK[0m
test_utils_statistics.R....... 6 tests [0;32mOK[0m
test_utils_statistics.R....... 7 tests [0;32mOK[0m [0;36m31ms[0m
test_utils_summarization.R.... 0 tests
test_utils_summarization.R.... 0 tests
test_utils_summarization.R.... 1 tests [0;32mOK[0m
test_utils_summarization.R.... 1 tests [0;32mOK[0m
test_utils_summarization.R.... 1 tests [0;32mOK[0m
test_utils_summarization.R.... 2 tests [0;32mOK[0m
test_utils_summarization.R.... 2 tests [0;32mOK[0m
test_utils_summarization.R.... 2 tests [0;32mOK[0m
test_utils_summarization.R.... 3 tests [0;32mOK[0m [0;36m7ms[0m
All ok, 91 results (14.4s)
>
> proc.time()
user system elapsed
6.594 0.482 17.672
MSstats.Rcheck/MSstats-Ex.timings
| name | user | system | elapsed | |
| DDARawData | 0.004 | 0.000 | 0.004 | |
| DDARawData.Skyline | 0.005 | 0.000 | 0.006 | |
| DIARawData | 0.003 | 0.000 | 0.003 | |
| MSstatsGroupComparison | 0.773 | 0.017 | 0.742 | |
| MSstatsGroupComparisonOutput | 0.342 | 0.043 | 0.338 | |
| MSstatsGroupComparisonSingleProtein | 0.301 | 0.019 | 0.252 | |
| MSstatsHandleMissing | 0.119 | 0.001 | 0.065 | |
| MSstatsMergeFractions | 0.111 | 0.001 | 0.058 | |
| MSstatsNormalize | 0.104 | 0.006 | 0.060 | |
| MSstatsPrepareForDataProcess | 0.090 | 0.012 | 0.057 | |
| MSstatsPrepareForGroupComparison | 0.230 | 0.000 | 0.181 | |
| MSstatsPrepareForSummarization | 0.097 | 0.000 | 0.053 | |
| MSstatsSelectFeatures | 0.383 | 0.004 | 0.259 | |
| MSstatsSummarizationOutput | 0.411 | 0.000 | 0.319 | |
| MSstatsSummarizeSingleLinear | 0.160 | 0.032 | 0.128 | |
| MSstatsSummarizeSingleTMP | 0.181 | 0.022 | 0.124 | |
| MSstatsSummarizeWithSingleCore | 0.370 | 0.065 | 0.353 | |
| SDRFtoAnnotation | 0.020 | 0.007 | 0.027 | |
| SRMRawData | 0.002 | 0.001 | 0.002 | |
| checkRepeatedDesign | 0.252 | 0.001 | 0.197 | |
| dataProcess | 0.645 | 0.031 | 0.534 | |
| dataProcessPlots | 7.871 | 0.213 | 7.968 | |
| designSampleSize | 0.334 | 0.010 | 0.297 | |
| designSampleSizePlots | 0.346 | 0.006 | 0.306 | |
| dot-makeQCPlot | 6.884 | 0.137 | 6.880 | |
| example_SDRF | 0.003 | 0.002 | 0.005 | |
| extractSDRF | 0.183 | 0.016 | 0.118 | |
| getProcessed | 0.130 | 0.006 | 0.069 | |
| getSamplesInfo | 0.446 | 0.013 | 0.339 | |
| groupComparison | 0.310 | 0.007 | 0.265 | |
| groupComparisonPlots | 3.375 | 0.010 | 3.330 | |
| groupComparisonQCPlots | 1.099 | 0.010 | 1.063 | |
| makePeptidesDictionary | 0.005 | 0.001 | 0.004 | |
| modelBasedQCPlots | 1.047 | 0.003 | 0.997 | |
| quantification | 0.243 | 0.003 | 0.202 | |